Starting phenix.real_space_refine on Sun Jul 5 02:37:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ub5_26435/07_2026/7ub5_26435.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ub5_26435/07_2026/7ub5_26435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ub5_26435/07_2026/7ub5_26435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ub5_26435/07_2026/7ub5_26435.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ub5_26435/07_2026/7ub5_26435.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ub5_26435/07_2026/7ub5_26435.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ub5_26435/07_2026/7ub5_26435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ub5_26435/07_2026/7ub5_26435.map" } resolution = 3.35 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= -0.004 sd= 0.148 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 113 5.16 5 C 15909 2.51 5 N 4081 2.21 5 O 4820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24923 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8216 Classifications: {'peptide': 1052} Link IDs: {'PTRANS': 50, 'TRANS': 1001} Chain breaks: 6 Chain: "B" Number of atoms: 8170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8170 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 50, 'TRANS': 993} Chain breaks: 6 Chain: "C" Number of atoms: 7879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7879 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 50, 'TRANS': 957} Chain breaks: 8 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.94, per 1000 atoms: 0.28 Number of scatterers: 24923 At special positions: 0 Unit cell: (138.24, 136.08, 178.2, 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 113 16.00 O 4820 8.00 N 4081 7.00 C 15909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 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 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 122 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1134 " " NAG B1310 " - " ASN B 717 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1134 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN C1098 " " NAG F 1 " - " ASN A 61 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1098 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN C 717 " " NAG N 1 " - " ASN C 801 " Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.1 seconds 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5810 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 44 sheets defined 26.4% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.112A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.993A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.866A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.555A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.286A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.710A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.363A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 844 through 847 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.283A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.738A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.157A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.975A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 383 through 387 removed outlier: 4.045A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.142A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.755A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.765A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 842 removed outlier: 3.995A pdb=" N ASP B 839 " --> pdb=" O LYS B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.658A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.832A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.783A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.768A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.783A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.662A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.360A pdb=" N LYS C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.031A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.876A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA C 956 " --> pdb=" O VAL C 952 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.321A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.929A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30 removed outlier: 7.556A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.762A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.002A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.322A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.496A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.794A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.212A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.554A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.861A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.561A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.013A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 29 through 30 removed outlier: 8.596A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.127A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.301A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.157A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 316 removed outlier: 6.992A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.567A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.723A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.150A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.861A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.919A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.403A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 29 through 30 removed outlier: 7.456A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.058A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.319A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.585A pdb=" N ALA C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.096A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.602A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.904A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 1048 hydrogen bonds defined for protein. 2865 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: 6.37 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7914 1.35 - 1.47: 6597 1.47 - 1.60: 10826 1.60 - 1.72: 1 1.72 - 1.85: 140 Bond restraints: 25478 Sorted by residual: bond pdb=" N VAL C 171 " pdb=" CA VAL C 171 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.14e-02 7.69e+03 1.02e+01 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.21e+00 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.62e+00 bond pdb=" N TYR C 170 " pdb=" CA TYR C 170 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.21e-02 6.83e+03 6.36e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.33e+00 ... (remaining 25473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 33286 1.55 - 3.09: 1160 3.09 - 4.64: 161 4.64 - 6.19: 23 6.19 - 7.74: 18 Bond angle restraints: 34648 Sorted by residual: angle pdb=" N ASN B 81 " pdb=" CA ASN B 81 " pdb=" C ASN B 81 " ideal model delta sigma weight residual 108.81 116.25 -7.44 2.23e+00 2.01e-01 1.11e+01 angle pdb=" CB GLU A1092 " pdb=" CG GLU A1092 " pdb=" CD GLU A1092 " ideal model delta sigma weight residual 112.60 118.25 -5.65 1.70e+00 3.46e-01 1.11e+01 angle pdb=" CA CYS C 391 " pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " ideal model delta sigma weight residual 114.40 121.71 -7.31 2.30e+00 1.89e-01 1.01e+01 angle pdb=" CA CYS B 391 " pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " ideal model delta sigma weight residual 114.40 121.67 -7.27 2.30e+00 1.89e-01 9.98e+00 angle pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " ideal model delta sigma weight residual 114.40 121.35 -6.95 2.30e+00 1.89e-01 9.12e+00 ... (remaining 34643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 13473 18.00 - 35.99: 1115 35.99 - 53.99: 156 53.99 - 71.99: 35 71.99 - 89.99: 18 Dihedral angle restraints: 14797 sinusoidal: 5765 harmonic: 9032 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -166.26 80.26 1 1.00e+01 1.00e-02 7.98e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -164.24 78.24 1 1.00e+01 1.00e-02 7.64e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -161.34 75.34 1 1.00e+01 1.00e-02 7.17e+01 ... (remaining 14794 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3648 0.092 - 0.183: 403 0.183 - 0.275: 12 0.275 - 0.367: 3 0.367 - 0.459: 2 Chirality restraints: 4068 Sorted by residual: chirality pdb=" CB ILE B 834 " pdb=" CA ILE B 834 " pdb=" CG1 ILE B 834 " pdb=" CG2 ILE B 834 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 4065 not shown) Planarity restraints: 4454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " 0.042 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO A 521 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 896 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.14e+00 pdb=" N PRO C 897 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 897 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 897 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " -0.023 2.00e-02 2.50e+03 2.19e-02 5.99e+00 pdb=" CG ASN B 709 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " 0.024 2.00e-02 2.50e+03 pdb=" C1 NAG B1307 " -0.024 2.00e-02 2.50e+03 ... (remaining 4451 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6754 2.81 - 3.33: 20017 3.33 - 3.85: 40829 3.85 - 4.38: 45608 4.38 - 4.90: 82623 Nonbonded interactions: 195831 Sorted by model distance: nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.287 3.040 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.305 3.040 nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.309 3.040 nonbonded pdb=" OG SER C 349 " pdb=" O LEU C 452 " model vdw 2.312 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.315 3.040 ... (remaining 195826 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 28 through 69 or resid 80 through 139 or resid 165 through \ 177 or resid 187 through 210 or resid 215 through 243 or resid 263 through 621 \ or resid 641 through 674 or resid 691 through 830 or resid 849 through 1308)) selection = (chain 'B' and (resid 28 through 69 or resid 80 through 139 or resid 165 through \ 177 or resid 187 through 210 or resid 215 through 243 or resid 263 through 674 \ or resid 691 through 830 or resid 849 through 1308)) selection = (chain 'C' and (resid 28 through 69 or resid 80 through 621 or resid 641 through \ 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 27.360 Find NCS groups from input model: 0.560 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 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 0.100 25566 Z= 0.204 Angle : 0.691 13.196 34871 Z= 0.359 Chirality : 0.053 0.459 4068 Planarity : 0.005 0.063 4417 Dihedral : 13.286 89.986 8864 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: -0.85 (0.14), residues: 3058 helix: -0.16 (0.17), residues: 712 sheet: 0.37 (0.18), residues: 716 loop : -1.18 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 237 TYR 0.037 0.001 TYR B 473 PHE 0.040 0.002 PHE B 392 TRP 0.017 0.001 TRP A 886 HIS 0.002 0.000 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.20 (25478) covalent geometry : angle 0.66567 / 0.35 (34648) SS BOND : bond 0.00465 / 0.30 ( 41) SS BOND : angle 1.29283 / 0.85 ( 82) hydrogen bonds : bond 0.05322 / 3.36 ( 1036) hydrogen bonds : angle 5.60124 / 3.84 ( 2865) link_BETA1-4 : bond 0.00743 / 0.49 ( 10) link_BETA1-4 : angle 2.68630 / 1.57 ( 30) link_NAG-ASN : bond 0.00517 / 0.37 ( 37) link_NAG-ASN : angle 2.91521 / 2.04 ( 111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 1.154 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1714 time to fit residues: 19.2308 Evaluate side-chains 54 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.0980 chunk 155 optimal weight: 0.0020 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 5.9990 overall best weight: 3.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 450 ASN A 613 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 762 GLN C 755 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.077319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.056116 restraints weight = 71340.675| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.74 r_work: 0.2750 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 25566 Z= 0.219 Angle : 0.569 10.255 34871 Z= 0.290 Chirality : 0.046 0.368 4068 Planarity : 0.004 0.041 4417 Dihedral : 4.318 19.420 3325 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.11 % Allowed : 3.67 % Favored : 96.22 % 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: -0.31 (0.15), residues: 3058 helix: 1.15 (0.20), residues: 708 sheet: 0.22 (0.18), residues: 714 loop : -1.01 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 237 TYR 0.020 0.002 TYR B1067 PHE 0.025 0.002 PHE A 906 TRP 0.011 0.001 TRP A 886 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.22 (25478) covalent geometry : angle 0.55213 / 0.29 (34648) SS BOND : bond 0.00365 / 0.22 ( 41) SS BOND : angle 1.01450 / 0.65 ( 82) hydrogen bonds : bond 0.04785 / 3.09 ( 1036) hydrogen bonds : angle 5.20750 / 3.56 ( 2865) link_BETA1-4 : bond 0.00145 / 0.09 ( 10) link_BETA1-4 : angle 1.73281 / 0.96 ( 30) link_NAG-ASN : bond 0.00335 / 0.23 ( 37) link_NAG-ASN : angle 2.25393 / 1.59 ( 111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8309 (mt0) outliers start: 3 outliers final: 1 residues processed: 57 average time/residue: 0.1666 time to fit residues: 16.7678 Evaluate side-chains 54 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 375 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 96 optimal weight: 0.9980 chunk 298 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 284 optimal weight: 0.8980 chunk 219 optimal weight: 10.0000 chunk 259 optimal weight: 5.9990 chunk 271 optimal weight: 4.9990 chunk 299 optimal weight: 3.9990 chunk 236 optimal weight: 5.9990 chunk 125 optimal weight: 0.6980 chunk 204 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 901 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.078260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.058335 restraints weight = 70433.863| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.90 r_work: 0.2782 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25566 Z= 0.109 Angle : 0.476 9.968 34871 Z= 0.243 Chirality : 0.043 0.368 4068 Planarity : 0.003 0.040 4417 Dihedral : 4.027 17.944 3325 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.11 % Allowed : 5.08 % Favored : 94.81 % 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: -0.00 (0.15), residues: 3058 helix: 1.66 (0.20), residues: 707 sheet: 0.28 (0.18), residues: 705 loop : -0.88 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 237 TYR 0.022 0.001 TYR C 170 PHE 0.013 0.001 PHE A 906 TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (25478) covalent geometry : angle 0.45919 / 0.24 (34648) SS BOND : bond 0.00311 / 0.21 ( 41) SS BOND : angle 0.86093 / 0.53 ( 82) hydrogen bonds : bond 0.03948 / 2.56 ( 1036) hydrogen bonds : angle 4.95536 / 3.38 ( 2865) link_BETA1-4 : bond 0.00290 / 0.18 ( 10) link_BETA1-4 : angle 1.73369 / 0.94 ( 30) link_NAG-ASN : bond 0.00293 / 0.21 ( 37) link_NAG-ASN : angle 2.02853 / 1.42 ( 111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 1.155 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 57 average time/residue: 0.1487 time to fit residues: 15.2564 Evaluate side-chains 57 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 64 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 294 optimal weight: 4.9990 chunk 217 optimal weight: 6.9990 chunk 233 optimal weight: 6.9990 chunk 271 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 227 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.077165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.057127 restraints weight = 70500.431| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.85 r_work: 0.2752 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 25566 Z= 0.166 Angle : 0.511 10.015 34871 Z= 0.259 Chirality : 0.044 0.359 4068 Planarity : 0.003 0.038 4417 Dihedral : 4.070 18.588 3325 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.37 % Allowed : 6.56 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.06 (0.15), residues: 3058 helix: 1.82 (0.20), residues: 708 sheet: 0.25 (0.19), residues: 700 loop : -0.85 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 78 TYR 0.018 0.001 TYR B1067 PHE 0.019 0.001 PHE A 906 TRP 0.010 0.001 TRP B 436 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (25478) covalent geometry : angle 0.49448 / 0.26 (34648) SS BOND : bond 0.00330 / 0.21 ( 41) SS BOND : angle 0.89109 / 0.56 ( 82) hydrogen bonds : bond 0.04328 / 2.80 ( 1036) hydrogen bonds : angle 5.01872 / 3.43 ( 2865) link_BETA1-4 : bond 0.00237 / 0.16 ( 10) link_BETA1-4 : angle 1.75011 / 0.95 ( 30) link_NAG-ASN : bond 0.00292 / 0.21 ( 37) link_NAG-ASN : angle 2.08140 / 1.46 ( 111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: C 1029 MET cc_start: 0.9329 (tpp) cc_final: 0.9093 (tpp) outliers start: 10 outliers final: 5 residues processed: 61 average time/residue: 0.1546 time to fit residues: 16.9759 Evaluate side-chains 58 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 415 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 77 optimal weight: 0.7980 chunk 303 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 239 optimal weight: 0.9990 chunk 262 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 286 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.078397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.058103 restraints weight = 70695.220| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.00 r_work: 0.2773 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25566 Z= 0.099 Angle : 0.459 9.694 34871 Z= 0.233 Chirality : 0.043 0.361 4068 Planarity : 0.003 0.039 4417 Dihedral : 3.863 17.144 3325 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.37 % Allowed : 7.16 % Favored : 92.47 % 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: 0.22 (0.15), residues: 3058 helix: 2.06 (0.20), residues: 701 sheet: 0.32 (0.19), residues: 699 loop : -0.78 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 815 TYR 0.017 0.001 TYR B1067 PHE 0.010 0.001 PHE B1121 TRP 0.009 0.001 TRP B 436 HIS 0.002 0.000 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (25478) covalent geometry : angle 0.44295 / 0.23 (34648) SS BOND : bond 0.00301 / 0.20 ( 41) SS BOND : angle 0.82043 / 0.50 ( 82) hydrogen bonds : bond 0.03731 / 2.42 ( 1036) hydrogen bonds : angle 4.82571 / 3.29 ( 2865) link_BETA1-4 : bond 0.00331 / 0.21 ( 10) link_BETA1-4 : angle 1.69689 / 0.92 ( 30) link_NAG-ASN : bond 0.00300 / 0.21 ( 37) link_NAG-ASN : angle 1.91644 / 1.34 ( 111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: C 1029 MET cc_start: 0.9335 (tpp) cc_final: 0.9104 (tpp) outliers start: 10 outliers final: 7 residues processed: 60 average time/residue: 0.1688 time to fit residues: 17.8282 Evaluate side-chains 60 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 154 optimal weight: 0.3980 chunk 194 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 238 optimal weight: 0.9980 chunk 302 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 198 optimal weight: 6.9990 chunk 301 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.077039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.056551 restraints weight = 71051.893| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.01 r_work: 0.2731 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 25566 Z= 0.170 Angle : 0.508 9.902 34871 Z= 0.257 Chirality : 0.044 0.349 4068 Planarity : 0.003 0.037 4417 Dihedral : 4.018 18.746 3325 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.44 % Allowed : 8.05 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.18 (0.15), residues: 3058 helix: 2.03 (0.20), residues: 707 sheet: 0.21 (0.19), residues: 699 loop : -0.78 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 646 TYR 0.022 0.001 TYR C 170 PHE 0.018 0.001 PHE A 906 TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (25478) covalent geometry : angle 0.49156 / 0.25 (34648) SS BOND : bond 0.00325 / 0.20 ( 41) SS BOND : angle 0.87970 / 0.54 ( 82) hydrogen bonds : bond 0.04334 / 2.81 ( 1036) hydrogen bonds : angle 4.98235 / 3.40 ( 2865) link_BETA1-4 : bond 0.00225 / 0.16 ( 10) link_BETA1-4 : angle 1.75302 / 0.95 ( 30) link_NAG-ASN : bond 0.00294 / 0.21 ( 37) link_NAG-ASN : angle 2.04900 / 1.43 ( 111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: C 1029 MET cc_start: 0.9336 (tpp) cc_final: 0.9101 (tpp) outliers start: 12 outliers final: 9 residues processed: 61 average time/residue: 0.1555 time to fit residues: 17.1462 Evaluate side-chains 60 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 415 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 104 optimal weight: 7.9990 chunk 253 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 218 optimal weight: 20.0000 chunk 181 optimal weight: 0.4980 chunk 242 optimal weight: 8.9990 chunk 194 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 189 optimal weight: 0.0670 chunk 294 optimal weight: 2.9990 overall best weight: 1.9124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.077288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.056909 restraints weight = 70666.693| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.96 r_work: 0.2740 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 25566 Z= 0.146 Angle : 0.491 9.722 34871 Z= 0.249 Chirality : 0.044 0.355 4068 Planarity : 0.003 0.037 4417 Dihedral : 3.980 18.443 3325 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.59 % Allowed : 8.31 % 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: 0.21 (0.15), residues: 3058 helix: 2.11 (0.20), residues: 700 sheet: 0.22 (0.19), residues: 691 loop : -0.77 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 815 TYR 0.019 0.001 TYR C 170 PHE 0.014 0.001 PHE A 906 TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (25478) covalent geometry : angle 0.47458 / 0.25 (34648) SS BOND : bond 0.00323 / 0.21 ( 41) SS BOND : angle 0.86258 / 0.52 ( 82) hydrogen bonds : bond 0.04142 / 2.68 ( 1036) hydrogen bonds : angle 4.93851 / 3.37 ( 2865) link_BETA1-4 : bond 0.00292 / 0.19 ( 10) link_BETA1-4 : angle 1.73547 / 0.93 ( 30) link_NAG-ASN : bond 0.00285 / 0.20 ( 37) link_NAG-ASN : angle 1.99821 / 1.40 ( 111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: C 1029 MET cc_start: 0.9326 (tpp) cc_final: 0.9084 (tpp) outliers start: 16 outliers final: 12 residues processed: 65 average time/residue: 0.1515 time to fit residues: 17.9237 Evaluate side-chains 63 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 415 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 117 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 232 optimal weight: 1.9990 chunk 281 optimal weight: 0.2980 chunk 68 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 156 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.3412 r_free = 0.3412 target = 0.076885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.055823 restraints weight = 70919.236| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.77 r_work: 0.2741 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 25566 Z= 0.166 Angle : 0.508 9.797 34871 Z= 0.257 Chirality : 0.044 0.351 4068 Planarity : 0.003 0.036 4417 Dihedral : 4.039 18.829 3325 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.67 % Allowed : 8.57 % Favored : 90.77 % 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: 0.18 (0.15), residues: 3058 helix: 2.10 (0.20), residues: 701 sheet: 0.13 (0.19), residues: 690 loop : -0.75 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 328 TYR 0.018 0.001 TYR B1067 PHE 0.016 0.001 PHE A 906 TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (25478) covalent geometry : angle 0.49172 / 0.25 (34648) SS BOND : bond 0.00331 / 0.21 ( 41) SS BOND : angle 0.89405 / 0.58 ( 82) hydrogen bonds : bond 0.04314 / 2.79 ( 1036) hydrogen bonds : angle 4.98554 / 3.40 ( 2865) link_BETA1-4 : bond 0.00250 / 0.17 ( 10) link_BETA1-4 : angle 1.77766 / 0.96 ( 30) link_NAG-ASN : bond 0.00296 / 0.21 ( 37) link_NAG-ASN : angle 2.04645 / 1.43 ( 111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: C 1029 MET cc_start: 0.9321 (tpp) cc_final: 0.9074 (tpp) outliers start: 18 outliers final: 15 residues processed: 62 average time/residue: 0.1545 time to fit residues: 17.3929 Evaluate side-chains 65 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 415 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.0346 > 50: distance: 64 - 160: 11.627 distance: 67 - 157: 7.108 distance: 79 - 147: 8.679 distance: 118 - 119: 11.019 distance: 119 - 120: 9.802 distance: 120 - 121: 10.354 distance: 120 - 122: 12.525 distance: 122 - 123: 11.085 distance: 123 - 126: 11.874 distance: 124 - 125: 10.214 distance: 124 - 129: 12.477 distance: 126 - 127: 6.430 distance: 126 - 128: 9.029 distance: 129 - 130: 3.612 distance: 130 - 131: 6.387 distance: 130 - 133: 3.158 distance: 131 - 132: 11.714 distance: 133 - 134: 4.000 distance: 134 - 136: 5.739 distance: 139 - 140: 4.029 distance: 141 - 142: 4.876 distance: 141 - 143: 3.704 distance: 144 - 145: 3.430 distance: 145 - 146: 5.367 distance: 146 - 147: 3.256 distance: 146 - 152: 6.198 distance: 149 - 150: 3.811 distance: 152 - 153: 15.486 distance: 153 - 154: 15.802 distance: 153 - 156: 16.918 distance: 154 - 155: 22.189 distance: 154 - 157: 10.851 distance: 157 - 158: 5.731 distance: 158 - 159: 6.039 distance: 158 - 161: 3.146 distance: 159 - 160: 6.695 distance: 159 - 164: 9.531 distance: 161 - 162: 9.753 distance: 161 - 163: 6.945 distance: 164 - 165: 5.849 distance: 165 - 166: 6.302 distance: 165 - 168: 5.339 distance: 166 - 172: 6.731 distance: 168 - 169: 7.376 distance: 169 - 170: 9.256 distance: 169 - 171: 7.671 distance: 172 - 173: 10.089 distance: 173 - 176: 4.289 distance: 174 - 175: 6.840 distance: 174 - 178: 3.537 distance: 176 - 177: 10.635 distance: 177 - 211: 5.589 distance: 178 - 179: 3.012 distance: 179 - 180: 6.083 distance: 179 - 182: 3.018 distance: 180 - 181: 7.868