Starting phenix.real_space_refine on Mon Aug 25 07:15:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vrw_32108/08_2025/7vrw_32108.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vrw_32108/08_2025/7vrw_32108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vrw_32108/08_2025/7vrw_32108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vrw_32108/08_2025/7vrw_32108.map" model { file = "/net/cci-nas-00/data/ceres_data/7vrw_32108/08_2025/7vrw_32108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vrw_32108/08_2025/7vrw_32108.cif" } resolution = 3.6 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16512 2.51 5 N 4260 2.21 5 O 5103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25989 Number of models: 1 Model: "" Number of chains: 20 Chain: "B" Number of atoms: 8397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8397 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1025} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 8397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8397 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1025} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 8397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8397 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1025} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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: "K" 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: "L" 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: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 5.28, per 1000 atoms: 0.20 Number of scatterers: 25989 At special positions: 0 Unit cell: (149.76, 157.04, 174.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 5103 8.00 N 4260 7.00 C 16512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 731 " - pdb=" SG CYS B 753 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B1025 " - pdb=" SG CYS B1036 " distance=2.03 Simple disulfide: pdb=" SG CYS B1075 " - pdb=" SG CYS B1119 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 731 " - pdb=" SG CYS A 753 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A1025 " - pdb=" SG CYS A1036 " distance=2.03 Simple disulfide: pdb=" SG CYS A1075 " - pdb=" SG CYS A1119 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 731 " - pdb=" SG CYS C 753 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C1025 " - pdb=" SG CYS C1036 " distance=2.03 Simple disulfide: pdb=" SG CYS C1075 " - pdb=" SG CYS C1119 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 702 " " NAG A1309 " - " ASN A1067 " " NAG A1310 " - " ASN A 165 " " NAG A1311 " - " ASN A 234 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 702 " " NAG B1307 " - " ASN B1067 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 61 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 702 " " NAG C1309 " - " ASN C1067 " " NAG D 1 " - " ASN B 234 " " NAG E 1 " - " ASN B 710 " " NAG F 1 " - " ASN B 794 " " NAG G 1 " - " ASN B1091 " " NAG H 1 " - " ASN B1127 " " NAG I 1 " - " ASN A 710 " " NAG J 1 " - " ASN A 794 " " NAG K 1 " - " ASN A1091 " " NAG L 1 " - " ASN A1127 " " NAG M 1 " - " ASN C 234 " " NAG N 1 " - " ASN C 710 " " NAG O 1 " - " ASN C 794 " " NAG P 1 " - " ASN C1091 " " NAG Q 1 " - " ASN C1127 " Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 747.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6036 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 57 sheets defined 23.8% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.805A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.064A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.226A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 418 through 423 removed outlier: 4.086A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 418 through 423' Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.649A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.874A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 735 Processing helix chain 'B' and resid 740 through 750 removed outlier: 3.628A pdb=" N GLY B 750 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 775 removed outlier: 3.598A pdb=" N GLN B 755 " --> pdb=" O SER B 751 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 775 " --> pdb=" O THR B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 816 Processing helix chain 'B' and resid 842 through 849 Processing helix chain 'B' and resid 859 through 877 Processing helix chain 'B' and resid 879 through 884 removed outlier: 4.120A pdb=" N ALA B 883 " --> pdb=" O TRP B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 903 removed outlier: 4.022A pdb=" N ALA B 896 " --> pdb=" O ALA B 892 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR B 897 " --> pdb=" O MET B 893 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG B 898 " --> pdb=" O GLN B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 912 removed outlier: 4.296A pdb=" N LEU B 909 " --> pdb=" O THR B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 932 Processing helix chain 'B' and resid 934 through 939 removed outlier: 3.911A pdb=" N ALA B 937 " --> pdb=" O THR B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 957 removed outlier: 3.697A pdb=" N ASN B 946 " --> pdb=" O GLN B 942 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN B 948 " --> pdb=" O VAL B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 961 removed outlier: 3.619A pdb=" N SER B 961 " --> pdb=" O GLN B 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 958 through 961' Processing helix chain 'B' and resid 978 through 1025 removed outlier: 5.038A pdb=" N VAL B 984 " --> pdb=" O PRO B 980 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN B 985 " --> pdb=" O GLU B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1140 removed outlier: 3.630A pdb=" N SER B1140 " --> pdb=" O PRO B1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.566A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.206A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.518A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.757A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.862A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 735 Processing helix chain 'A' and resid 740 through 750 removed outlier: 3.512A pdb=" N GLY A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 775 removed outlier: 3.574A pdb=" N GLN A 755 " --> pdb=" O SER A 751 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 775 " --> pdb=" O THR A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 816 Processing helix chain 'A' and resid 842 through 849 Processing helix chain 'A' and resid 859 through 878 Processing helix chain 'A' and resid 879 through 884 removed outlier: 4.061A pdb=" N ALA A 883 " --> pdb=" O TRP A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 902 removed outlier: 3.824A pdb=" N ALA A 896 " --> pdb=" O ALA A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 912 removed outlier: 4.154A pdb=" N LEU A 909 " --> pdb=" O THR A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 932 Processing helix chain 'A' and resid 934 through 939 removed outlier: 3.939A pdb=" N ALA A 937 " --> pdb=" O THR A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 957 removed outlier: 3.816A pdb=" N ASN A 946 " --> pdb=" O GLN A 942 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASN A 948 " --> pdb=" O VAL A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 961 removed outlier: 3.559A pdb=" N SER A 961 " --> pdb=" O GLN A 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 958 through 961' Processing helix chain 'A' and resid 978 through 1025 removed outlier: 5.141A pdb=" N VAL A 984 " --> pdb=" O PRO A 980 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN A 985 " --> pdb=" O GLU A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1140 removed outlier: 3.744A pdb=" N SER A1140 " --> pdb=" O PRO A1136 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.764A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN C 343 " --> pdb=" O GLY C 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 338 through 343' Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.200A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 418 through 423 removed outlier: 3.870A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.646A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.871A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 740 through 750 removed outlier: 3.545A pdb=" N GLY C 750 " --> pdb=" O LEU C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 775 removed outlier: 3.559A pdb=" N GLN C 755 " --> pdb=" O SER C 751 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C 775 " --> pdb=" O THR C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 816 Processing helix chain 'C' and resid 842 through 849 Processing helix chain 'C' and resid 859 through 878 Processing helix chain 'C' and resid 879 through 884 removed outlier: 4.138A pdb=" N ALA C 883 " --> pdb=" O TRP C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 890 through 902 removed outlier: 3.942A pdb=" N ALA C 896 " --> pdb=" O ALA C 892 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR C 897 " --> pdb=" O MET C 893 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN C 900 " --> pdb=" O ALA C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 912 removed outlier: 4.146A pdb=" N LEU C 909 " --> pdb=" O THR C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 932 Processing helix chain 'C' and resid 934 through 939 removed outlier: 3.906A pdb=" N ALA C 937 " --> pdb=" O THR C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 957 removed outlier: 3.769A pdb=" N ASN C 946 " --> pdb=" O GLN C 942 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN C 948 " --> pdb=" O VAL C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 961 removed outlier: 3.571A pdb=" N SER C 961 " --> pdb=" O GLN C 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 958 through 961' Processing helix chain 'C' and resid 978 through 1025 removed outlier: 4.927A pdb=" N VAL C 984 " --> pdb=" O PRO C 980 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN C 985 " --> pdb=" O GLU C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 1134 through 1140 removed outlier: 3.814A pdb=" N SER C1140 " --> pdb=" O PRO C1136 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.608A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.554A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.643A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'B' and resid 118 through 120 removed outlier: 3.589A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.736A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AA9, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.801A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'B' and resid 539 through 540 removed outlier: 3.714A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 670 through 675 removed outlier: 3.607A pdb=" N SER B 684 " --> pdb=" O GLN B 675 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 694 through 695 removed outlier: 6.560A pdb=" N ALA B 694 " --> pdb=" O ILE C 781 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 704 through 706 Processing sheet with id=AB6, first strand: chain 'B' and resid 710 through 713 removed outlier: 6.564A pdb=" N ASN B 710 " --> pdb=" O ALA B1063 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 710 through 713 removed outlier: 6.564A pdb=" N ASN B 710 " --> pdb=" O ALA B1063 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLY B1052 " --> pdb=" O SER B1048 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N SER B1048 " --> pdb=" O GLY B1052 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B1054 " --> pdb=" O PRO B1046 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU B1056 " --> pdb=" O SER B1044 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER B1044 " --> pdb=" O LEU B1056 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL B1058 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 726 through 729 removed outlier: 4.274A pdb=" N LYS B 726 " --> pdb=" O LEU B 854 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 780 through 781 Processing sheet with id=AC1, first strand: chain 'B' and resid 1074 through 1075 Processing sheet with id=AC2, first strand: chain 'B' and resid 1079 through 1083 removed outlier: 4.554A pdb=" N ALA B1080 " --> pdb=" O SER B1116 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B1116 " --> pdb=" O ALA B1080 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1087 through 1089 Processing sheet with id=AC4, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.948A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.522A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AC7, first strand: chain 'A' and resid 101 through 107 removed outlier: 6.244A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 118 through 120 removed outlier: 3.631A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.544A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 327 through 328 Processing sheet with id=AD2, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.793A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'A' and resid 539 through 540 removed outlier: 3.774A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 670 through 675 removed outlier: 3.591A pdb=" N SER A 684 " --> pdb=" O GLN A 675 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 704 through 712 removed outlier: 6.618A pdb=" N SER A 704 " --> pdb=" O THR A1069 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR A1069 " --> pdb=" O SER A 704 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA A 706 " --> pdb=" O ASN A1067 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN A1067 " --> pdb=" O ALA A 706 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU A1065 " --> pdb=" O PRO A 708 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN A 710 " --> pdb=" O ALA A1063 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 704 through 712 removed outlier: 6.618A pdb=" N SER A 704 " --> pdb=" O THR A1069 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR A1069 " --> pdb=" O SER A 704 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA A 706 " --> pdb=" O ASN A1067 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN A1067 " --> pdb=" O ALA A 706 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU A1065 " --> pdb=" O PRO A 708 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN A 710 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A1052 " --> pdb=" O ALA A1049 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A1049 " --> pdb=" O GLY A1052 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N TYR A1060 " --> pdb=" O HIS A1041 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N HIS A1041 " --> pdb=" O TYR A1060 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 726 through 729 removed outlier: 4.276A pdb=" N LYS A 726 " --> pdb=" O LEU A 854 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 780 through 781 Processing sheet with id=AE1, first strand: chain 'A' and resid 1074 through 1075 Processing sheet with id=AE2, first strand: chain 'A' and resid 1079 through 1083 removed outlier: 4.518A pdb=" N ALA A1080 " --> pdb=" O SER A1116 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A1116 " --> pdb=" O ALA A1080 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 1087 through 1089 Processing sheet with id=AE4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.438A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 48 through 51 Processing sheet with id=AE6, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE7, first strand: chain 'C' and resid 101 through 107 removed outlier: 6.465A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 118 through 120 removed outlier: 3.715A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.741A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 327 through 328 Processing sheet with id=AF2, first strand: chain 'C' and resid 356 through 358 removed outlier: 4.028A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF4, first strand: chain 'C' and resid 539 through 540 removed outlier: 3.705A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.481A pdb=" N GLU C 654 " --> pdb=" O ALA C 687 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N THR C 689 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER C 684 " --> pdb=" O GLN C 675 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 704 through 706 Processing sheet with id=AF7, first strand: chain 'C' and resid 710 through 712 removed outlier: 6.687A pdb=" N ASN C 710 " --> pdb=" O ALA C1063 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL C1058 " --> pdb=" O LEU C1042 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 715 through 721 removed outlier: 3.636A pdb=" N GLY C1052 " --> pdb=" O ALA C1049 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C1049 " --> pdb=" O GLY C1052 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 726 through 729 removed outlier: 4.331A pdb=" N LYS C 726 " --> pdb=" O LEU C 854 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 1074 through 1075 Processing sheet with id=AG2, first strand: chain 'C' and resid 1079 through 1083 removed outlier: 4.511A pdb=" N ALA C1080 " --> pdb=" O SER C1116 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C1116 " --> pdb=" O ALA C1080 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 1087 through 1090 825 hydrogen bonds defined for protein. 2274 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: 4.37 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8269 1.34 - 1.47: 6825 1.47 - 1.60: 11336 1.60 - 1.73: 0 1.73 - 1.86: 144 Bond restraints: 26574 Sorted by residual: bond pdb=" N VAL B 615 " pdb=" CA VAL B 615 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.14e-02 7.69e+03 1.30e+01 bond pdb=" N VAL B 62 " pdb=" CA VAL B 62 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.17e-02 7.31e+03 8.41e+00 bond pdb=" N SER B 60 " pdb=" CA SER B 60 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.34e-02 5.57e+03 6.48e+00 bond pdb=" N CYS B 617 " pdb=" CA CYS B 617 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.15e-02 7.56e+03 6.31e+00 bond pdb=" N ASN B 616 " pdb=" CA ASN B 616 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.42e-02 4.96e+03 4.83e+00 ... (remaining 26569 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 35026 1.72 - 3.44: 1031 3.44 - 5.16: 82 5.16 - 6.88: 21 6.88 - 8.60: 8 Bond angle restraints: 36168 Sorted by residual: angle pdb=" N ILE B 418 " pdb=" CA ILE B 418 " pdb=" C ILE B 418 " ideal model delta sigma weight residual 113.20 108.39 4.81 9.60e-01 1.09e+00 2.51e+01 angle pdb=" N ILE C 418 " pdb=" CA ILE C 418 " pdb=" C ILE C 418 " ideal model delta sigma weight residual 113.71 109.72 3.99 9.50e-01 1.11e+00 1.77e+01 angle pdb=" CA CYS C 379 " pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " ideal model delta sigma weight residual 114.40 122.02 -7.62 2.30e+00 1.89e-01 1.10e+01 angle pdb=" CA CYS A 379 " pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 114.40 121.98 -7.58 2.30e+00 1.89e-01 1.09e+01 angle pdb=" N GLY C 311 " pdb=" CA GLY C 311 " pdb=" C GLY C 311 " ideal model delta sigma weight residual 111.85 115.31 -3.46 1.06e+00 8.90e-01 1.07e+01 ... (remaining 36163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.14: 15521 23.14 - 46.29: 862 46.29 - 69.43: 120 69.43 - 92.58: 26 92.58 - 115.72: 22 Dihedral angle restraints: 16551 sinusoidal: 7152 harmonic: 9399 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -0.61 -85.39 1 1.00e+01 1.00e-02 8.83e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -9.93 -76.07 1 1.00e+01 1.00e-02 7.29e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -24.88 -61.12 1 1.00e+01 1.00e-02 4.96e+01 ... (remaining 16548 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 4106 0.103 - 0.206: 141 0.206 - 0.308: 8 0.308 - 0.411: 0 0.411 - 0.514: 2 Chirality restraints: 4257 Sorted by residual: chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.61e+00 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 657 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.80e+00 chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A 657 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 4254 not shown) Planarity restraints: 4663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1309 " -0.125 2.00e-02 2.50e+03 1.04e-01 1.35e+02 pdb=" C7 NAG B1309 " 0.036 2.00e-02 2.50e+03 pdb=" C8 NAG B1309 " -0.095 2.00e-02 2.50e+03 pdb=" N2 NAG B1309 " 0.167 2.00e-02 2.50e+03 pdb=" O7 NAG B1309 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 138 " -0.087 5.00e-02 4.00e+02 1.32e-01 2.79e+01 pdb=" N PRO B 139 " 0.229 5.00e-02 4.00e+02 pdb=" CA PRO B 139 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 139 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1308 " 0.052 2.00e-02 2.50e+03 4.64e-02 2.69e+01 pdb=" C7 NAG B1308 " -0.006 2.00e-02 2.50e+03 pdb=" C8 NAG B1308 " -0.009 2.00e-02 2.50e+03 pdb=" N2 NAG B1308 " -0.079 2.00e-02 2.50e+03 pdb=" O7 NAG B1308 " 0.041 2.00e-02 2.50e+03 ... (remaining 4660 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 784 2.70 - 3.25: 26089 3.25 - 3.80: 40164 3.80 - 4.35: 51932 4.35 - 4.90: 87040 Nonbonded interactions: 206009 Sorted by model distance: nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.154 3.040 nonbonded pdb=" O LYS B 113 " pdb=" OG SER A 469 " model vdw 2.162 3.040 nonbonded pdb=" NE2 GLN B 563 " pdb=" O LYS C 41 " model vdw 2.184 3.120 nonbonded pdb=" OG SER B 469 " pdb=" O LYS C 113 " model vdw 2.189 3.040 nonbonded pdb=" OG1 THR B 385 " pdb=" OG1 THR A 415 " model vdw 2.194 3.040 ... (remaining 206004 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 27 through 1309) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } 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 group one per residue 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.530 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 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 0.055 26670 Z= 0.186 Angle : 0.701 16.590 36417 Z= 0.369 Chirality : 0.046 0.514 4257 Planarity : 0.005 0.132 4620 Dihedral : 14.533 115.724 10398 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.04 % Allowed : 0.18 % Favored : 99.79 % 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 aren not related in a simple way. whole: -2.22 (0.14), residues: 3213 helix: 0.52 (0.21), residues: 705 sheet: -1.95 (0.19), residues: 660 loop : -2.17 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 319 TYR 0.019 0.001 TYR C 700 PHE 0.029 0.001 PHE A 562 TRP 0.017 0.001 TRP B 436 HIS 0.010 0.001 HIS B1041 Details of bonding type rmsd covalent geometry : bond 0.00366 (26574) covalent geometry : angle 0.66584 (36168) SS BOND : bond 0.00595 ( 39) SS BOND : angle 1.82255 ( 78) hydrogen bonds : bond 0.16105 ( 817) hydrogen bonds : angle 7.29550 ( 2274) link_BETA1-4 : bond 0.00662 ( 14) link_BETA1-4 : angle 2.93651 ( 42) link_NAG-ASN : bond 0.00609 ( 43) link_NAG-ASN : angle 3.09384 ( 129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 355 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.5499 (mmm) cc_final: 0.5189 (mmm) REVERT: B 177 MET cc_start: 0.3929 (mmm) cc_final: 0.1251 (tmm) REVERT: B 398 ASP cc_start: 0.6907 (m-30) cc_final: 0.6454 (m-30) REVERT: B 733 MET cc_start: 0.7440 (tpp) cc_final: 0.6880 (mmm) REVERT: A 353 TRP cc_start: 0.8045 (p90) cc_final: 0.7732 (p90) REVERT: A 927 ILE cc_start: 0.8411 (tp) cc_final: 0.8207 (tp) REVERT: A 950 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8023 (tm-30) REVERT: A 1128 ASN cc_start: 0.7994 (t0) cc_final: 0.7721 (t0) outliers start: 1 outliers final: 0 residues processed: 355 average time/residue: 0.1341 time to fit residues: 80.5059 Evaluate side-chains 236 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 644 GLN B 658 ASN ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 ASN A 777 GLN ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 HIS A1099 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 644 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.171764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.142776 restraints weight = 40279.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.142570 restraints weight = 50962.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.143785 restraints weight = 43496.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.144659 restraints weight = 30852.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.144868 restraints weight = 32413.482| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26670 Z= 0.177 Angle : 0.663 15.678 36417 Z= 0.325 Chirality : 0.047 0.426 4257 Planarity : 0.005 0.095 4620 Dihedral : 9.196 104.625 4665 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.49 % Allowed : 8.72 % Favored : 89.79 % 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 aren not related in a simple way. whole: -2.23 (0.14), residues: 3213 helix: 0.38 (0.20), residues: 714 sheet: -1.91 (0.19), residues: 699 loop : -2.13 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 246 TYR 0.016 0.001 TYR C 700 PHE 0.022 0.002 PHE A 592 TRP 0.010 0.001 TRP A 436 HIS 0.016 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00414 (26574) covalent geometry : angle 0.63070 (36168) SS BOND : bond 0.00579 ( 39) SS BOND : angle 1.78947 ( 78) hydrogen bonds : bond 0.03949 ( 817) hydrogen bonds : angle 5.82438 ( 2274) link_BETA1-4 : bond 0.00493 ( 14) link_BETA1-4 : angle 2.58501 ( 42) link_NAG-ASN : bond 0.00604 ( 43) link_NAG-ASN : angle 2.88302 ( 129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 257 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 398 ASP cc_start: 0.6976 (m-30) cc_final: 0.6685 (m-30) REVERT: B 877 SER cc_start: 0.8792 (t) cc_final: 0.8467 (p) REVERT: A 353 TRP cc_start: 0.8266 (p90) cc_final: 0.7878 (p90) REVERT: A 718 GLU cc_start: 0.7947 (tp30) cc_final: 0.7742 (tt0) REVERT: A 733 MET cc_start: 0.7369 (mmm) cc_final: 0.7127 (mmm) REVERT: A 927 ILE cc_start: 0.8592 (tp) cc_final: 0.8385 (tp) REVERT: A 950 GLN cc_start: 0.8476 (tm-30) cc_final: 0.7913 (tm-30) REVERT: C 950 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7734 (tm-30) REVERT: C 1131 TYR cc_start: 0.8161 (t80) cc_final: 0.7906 (t80) outliers start: 42 outliers final: 35 residues processed: 276 average time/residue: 0.1264 time to fit residues: 59.1799 Evaluate side-chains 249 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 724 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 768 ASP Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1097 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 22 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 110 optimal weight: 20.0000 chunk 52 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 293 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 138 optimal weight: 9.9990 chunk 265 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 644 GLN ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 ASN ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 HIS A1099 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 658 ASN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.173927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.144430 restraints weight = 40197.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.144091 restraints weight = 51109.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.145076 restraints weight = 43178.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.147798 restraints weight = 31276.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.147849 restraints weight = 23858.960| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26670 Z= 0.118 Angle : 0.603 15.659 36417 Z= 0.294 Chirality : 0.045 0.419 4257 Planarity : 0.004 0.061 4620 Dihedral : 8.343 105.121 4665 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.60 % Allowed : 11.92 % Favored : 86.48 % 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 aren not related in a simple way. whole: -1.93 (0.14), residues: 3213 helix: 0.69 (0.20), residues: 708 sheet: -1.62 (0.19), residues: 669 loop : -2.01 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 357 TYR 0.018 0.001 TYR C1103 PHE 0.019 0.001 PHE C 541 TRP 0.008 0.001 TRP B 436 HIS 0.010 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00269 (26574) covalent geometry : angle 0.56953 (36168) SS BOND : bond 0.00572 ( 39) SS BOND : angle 1.69513 ( 78) hydrogen bonds : bond 0.03581 ( 817) hydrogen bonds : angle 5.43543 ( 2274) link_BETA1-4 : bond 0.00584 ( 14) link_BETA1-4 : angle 2.58428 ( 42) link_NAG-ASN : bond 0.00549 ( 43) link_NAG-ASN : angle 2.80918 ( 129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 269 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.4246 (mmm) cc_final: 0.1417 (tmm) REVERT: B 398 ASP cc_start: 0.6909 (m-30) cc_final: 0.6706 (m-30) REVERT: B 514 SER cc_start: 0.8376 (m) cc_final: 0.7869 (p) REVERT: B 733 MET cc_start: 0.7762 (mmm) cc_final: 0.7537 (mmm) REVERT: B 877 SER cc_start: 0.8717 (t) cc_final: 0.8419 (p) REVERT: B 950 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8144 (tm-30) REVERT: B 987 ASP cc_start: 0.6549 (m-30) cc_final: 0.6096 (m-30) REVERT: A 353 TRP cc_start: 0.8206 (p90) cc_final: 0.7895 (p90) REVERT: A 927 ILE cc_start: 0.8488 (tp) cc_final: 0.8271 (tp) REVERT: A 950 GLN cc_start: 0.8430 (tm-30) cc_final: 0.7791 (tm-30) REVERT: C 88 ASP cc_start: 0.7304 (p0) cc_final: 0.7054 (p0) REVERT: C 660 TYR cc_start: 0.7456 (m-10) cc_final: 0.6983 (m-80) REVERT: C 818 LYS cc_start: 0.7489 (mtmm) cc_final: 0.7068 (ptmt) REVERT: C 950 GLN cc_start: 0.8214 (tm-30) cc_final: 0.7634 (tm-30) REVERT: C 1131 TYR cc_start: 0.8132 (t80) cc_final: 0.7906 (t80) outliers start: 45 outliers final: 32 residues processed: 293 average time/residue: 0.1276 time to fit residues: 62.8800 Evaluate side-chains 261 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 229 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 768 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 84 optimal weight: 3.9990 chunk 271 optimal weight: 5.9990 chunk 129 optimal weight: 0.0770 chunk 285 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 154 optimal weight: 0.4980 chunk 123 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 580 GLN B 658 ASN B 928 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 ASN ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 HIS A1099 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 409 GLN C 658 ASN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.173526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.144296 restraints weight = 39954.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.143634 restraints weight = 51619.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.145468 restraints weight = 41183.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.145758 restraints weight = 30780.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.146223 restraints weight = 30901.303| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26670 Z= 0.124 Angle : 0.597 15.668 36417 Z= 0.289 Chirality : 0.045 0.419 4257 Planarity : 0.004 0.046 4620 Dihedral : 7.736 101.685 4665 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.96 % Allowed : 13.91 % Favored : 84.13 % 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 aren not related in a simple way. whole: -1.78 (0.15), residues: 3213 helix: 0.80 (0.20), residues: 708 sheet: -1.52 (0.20), residues: 660 loop : -1.92 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.021 0.001 TYR C1103 PHE 0.025 0.001 PHE B 140 TRP 0.008 0.001 TRP B 436 HIS 0.009 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00288 (26574) covalent geometry : angle 0.56489 (36168) SS BOND : bond 0.00324 ( 39) SS BOND : angle 1.49976 ( 78) hydrogen bonds : bond 0.03435 ( 817) hydrogen bonds : angle 5.25890 ( 2274) link_BETA1-4 : bond 0.00606 ( 14) link_BETA1-4 : angle 2.59328 ( 42) link_NAG-ASN : bond 0.00598 ( 43) link_NAG-ASN : angle 2.73669 ( 129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 256 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.4131 (mmm) cc_final: 0.1277 (tmm) REVERT: B 398 ASP cc_start: 0.6884 (m-30) cc_final: 0.6619 (m-30) REVERT: B 514 SER cc_start: 0.8384 (m) cc_final: 0.7941 (p) REVERT: B 602 THR cc_start: 0.7420 (OUTLIER) cc_final: 0.7127 (p) REVERT: B 660 TYR cc_start: 0.6896 (m-80) cc_final: 0.6375 (m-80) REVERT: B 877 SER cc_start: 0.8733 (t) cc_final: 0.8437 (p) REVERT: B 950 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8118 (tm-30) REVERT: B 987 ASP cc_start: 0.6553 (m-30) cc_final: 0.6113 (m-30) REVERT: A 65 PHE cc_start: 0.7469 (m-10) cc_final: 0.7235 (m-10) REVERT: A 177 MET cc_start: 0.4756 (tmm) cc_final: 0.4458 (tmm) REVERT: A 353 TRP cc_start: 0.8245 (p90) cc_final: 0.7995 (p90) REVERT: A 927 ILE cc_start: 0.8507 (tp) cc_final: 0.8262 (tp) REVERT: A 950 GLN cc_start: 0.8438 (tm-30) cc_final: 0.7749 (tm-30) REVERT: C 88 ASP cc_start: 0.7054 (p0) cc_final: 0.6769 (p0) REVERT: C 660 TYR cc_start: 0.7406 (m-10) cc_final: 0.6946 (m-80) REVERT: C 950 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7642 (tm-30) REVERT: C 1131 TYR cc_start: 0.8125 (t80) cc_final: 0.7895 (t80) outliers start: 55 outliers final: 43 residues processed: 287 average time/residue: 0.1288 time to fit residues: 63.3265 Evaluate side-chains 272 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 228 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 724 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 768 ASP Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1097 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.5587 > 50: distance: 30 - 34: 14.434 distance: 34 - 35: 6.859 distance: 34 - 170: 17.802 distance: 35 - 36: 12.266 distance: 35 - 38: 30.290 distance: 36 - 37: 18.374 distance: 36 - 41: 17.526 distance: 37 - 167: 21.744 distance: 38 - 39: 8.903 distance: 38 - 40: 29.268 distance: 41 - 42: 23.698 distance: 42 - 43: 24.988 distance: 42 - 45: 7.609 distance: 43 - 44: 15.878 distance: 43 - 52: 9.258 distance: 45 - 46: 11.225 distance: 46 - 47: 14.172 distance: 46 - 48: 7.295 distance: 47 - 49: 17.428 distance: 48 - 50: 13.545 distance: 49 - 51: 12.765 distance: 50 - 51: 15.482 distance: 52 - 53: 18.647 distance: 52 - 156: 22.908 distance: 53 - 54: 10.103 distance: 53 - 56: 27.066 distance: 54 - 55: 16.415 distance: 54 - 61: 12.430 distance: 55 - 153: 16.246 distance: 56 - 57: 17.380 distance: 57 - 58: 8.618 distance: 58 - 59: 19.256 distance: 59 - 60: 10.983 distance: 61 - 62: 9.805 distance: 62 - 63: 11.836 distance: 62 - 65: 16.652 distance: 63 - 64: 9.159 distance: 63 - 67: 11.523 distance: 65 - 66: 22.191 distance: 66 - 152: 26.899 distance: 67 - 68: 11.021 distance: 68 - 71: 3.891 distance: 69 - 70: 24.858 distance: 69 - 79: 7.634 distance: 71 - 72: 15.177 distance: 72 - 73: 22.240 distance: 72 - 74: 14.683 distance: 73 - 75: 5.372 distance: 74 - 76: 6.926 distance: 75 - 77: 8.874 distance: 76 - 77: 8.408 distance: 77 - 78: 4.703 distance: 79 - 80: 5.829 distance: 80 - 81: 8.340 distance: 81 - 82: 17.872 distance: 81 - 83: 6.164 distance: 83 - 84: 29.699 distance: 84 - 85: 5.375 distance: 84 - 87: 28.525 distance: 85 - 86: 28.327 distance: 85 - 90: 22.440 distance: 87 - 88: 36.046 distance: 87 - 89: 8.996 distance: 90 - 91: 4.661 distance: 91 - 92: 13.764 distance: 91 - 94: 37.093 distance: 92 - 93: 25.705 distance: 92 - 96: 24.727 distance: 93 - 110: 23.831 distance: 94 - 95: 27.533 distance: 96 - 97: 13.413 distance: 96 - 102: 31.614 distance: 97 - 98: 7.050 distance: 97 - 100: 30.894 distance: 98 - 99: 18.728 distance: 100 - 101: 16.975 distance: 101 - 102: 53.717 distance: 103 - 104: 33.817 distance: 104 - 105: 32.062 distance: 104 - 107: 28.119 distance: 105 - 106: 27.268 distance: 105 - 110: 21.232 distance: 107 - 108: 17.684 distance: 107 - 109: 27.231