Starting phenix.real_space_refine on Thu Jun 19 21:10:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dt8_27692/06_2025/8dt8_27692.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dt8_27692/06_2025/8dt8_27692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dt8_27692/06_2025/8dt8_27692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dt8_27692/06_2025/8dt8_27692.map" model { file = "/net/cci-nas-00/data/ceres_data/8dt8_27692/06_2025/8dt8_27692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dt8_27692/06_2025/8dt8_27692.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 108 5.16 5 C 14506 2.51 5 N 3775 2.21 5 O 4407 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22796 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7939 Classifications: {'peptide': 1015} Link IDs: {'PTRANS': 54, 'TRANS': 960} Chain breaks: 7 Chain: "H" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 982 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "D" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 941 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "C" Number of atoms: 6377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6377 Classifications: {'peptide': 818} Link IDs: {'PTRANS': 43, 'TRANS': 774} Chain breaks: 8 Chain: "B" Number of atoms: 6375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6375 Classifications: {'peptide': 818} Link IDs: {'PTRANS': 45, 'TRANS': 772} Chain breaks: 8 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 12.97, per 1000 atoms: 0.57 Number of scatterers: 22796 At special positions: 0 Unit cell: (140.03, 136.895, 204.82, 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 108 16.00 O 4407 8.00 N 3775 7.00 C 14506 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=1.90 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 705 " - pdb=" SG CYS B 883 " 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 A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS H 49 " - pdb=" SG CYS H 69 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 69 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.04 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 C 883 " - pdb=" SG CYS B 705 " distance=2.04 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 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 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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 NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 801 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A1098 " " NAG B1301 " - " ASN B 717 " " NAG B1302 " - " ASN B 801 " " NAG B1303 " - " ASN B1098 " " NAG C1301 " - " ASN C 717 " " NAG C1302 " - " ASN C 801 " " NAG C1303 " - " ASN C1134 " " NAG C1304 " - " ASN C1098 " Time building additional restraints: 5.82 Conformation dependent library (CDL) restraints added in 2.7 seconds 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5418 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 43 sheets defined 24.0% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.373A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.081A 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 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.573A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (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 removed outlier: 3.745A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.018A 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 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 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 1033 removed outlier: 4.691A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.016A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.720A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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 1033 removed outlier: 3.886A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.064A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.440A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.194A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.784A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.508A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 317 removed outlier: 7.050A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.719A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.495A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.394A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.241A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.241A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.538A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.806A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 7 through 8 removed outlier: 3.553A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.313A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.313A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASP H 100I" --> pdb=" O TYR H 96 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.373A pdb=" N GLY D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N MET D 34 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ALA D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 29 through 30 removed outlier: 7.763A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 42 through 44 removed outlier: 3.588A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.770A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.539A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.265A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.576A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.531A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.531A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.458A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 787 through 789 Processing sheet with id=AD4, first strand: chain 'C' and resid 796 through 797 Processing sheet with id=AD5, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.642A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.176A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.765A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 83 through 85 removed outlier: 7.009A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.312A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.691A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.337A pdb=" N TYR B 660 " --> pdb=" O SER B 698 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.553A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.277A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.277A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.344A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.669A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) 1031 hydrogen bonds defined for protein. 2841 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: 10.14 Time building geometry restraints manager: 6.51 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: 7330 1.35 - 1.47: 5860 1.47 - 1.59: 9978 1.59 - 1.72: 0 1.72 - 1.84: 137 Bond restraints: 23305 Sorted by residual: bond pdb=" N PRO B 986 " pdb=" CA PRO B 986 " ideal model delta sigma weight residual 1.465 1.506 -0.041 2.03e-02 2.43e+03 4.10e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.89e+00 bond pdb=" CG LEU C 916 " pdb=" CD2 LEU C 916 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.85e+00 bond pdb=" C1 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.72e+00 bond pdb=" CG LEU A 916 " pdb=" CD2 LEU A 916 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.70e+00 ... (remaining 23300 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 29742 1.89 - 3.77: 1677 3.77 - 5.66: 259 5.66 - 7.55: 19 7.55 - 9.44: 3 Bond angle restraints: 31700 Sorted by residual: angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.13 -5.43 1.22e+00 6.72e-01 1.98e+01 angle pdb=" N GLN C 613 " pdb=" CA GLN C 613 " pdb=" C GLN C 613 " ideal model delta sigma weight residual 111.28 116.13 -4.85 1.09e+00 8.42e-01 1.98e+01 angle pdb=" N ARG C 214 " pdb=" CA ARG C 214 " pdb=" C ARG C 214 " ideal model delta sigma weight residual 110.80 120.24 -9.44 2.13e+00 2.20e-01 1.96e+01 angle pdb=" N LEU A 117 " pdb=" CA LEU A 117 " pdb=" C LEU A 117 " ideal model delta sigma weight residual 109.46 116.16 -6.70 1.66e+00 3.63e-01 1.63e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 115.50 -4.80 1.22e+00 6.72e-01 1.55e+01 ... (remaining 31695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 13496 17.43 - 34.86: 413 34.86 - 52.28: 94 52.28 - 69.71: 60 69.71 - 87.14: 20 Dihedral angle restraints: 14083 sinusoidal: 5667 harmonic: 8416 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -160.01 74.01 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 37.28 55.72 1 1.00e+01 1.00e-02 4.19e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 92 " pdb=" CB CYS D 92 " ideal model delta sinusoidal sigma weight residual 93.00 136.09 -43.09 1 1.00e+01 1.00e-02 2.59e+01 ... (remaining 14080 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2266 0.045 - 0.089: 948 0.089 - 0.134: 320 0.134 - 0.178: 83 0.178 - 0.223: 14 Chirality restraints: 3631 Sorted by residual: chirality pdb=" CA PHE D 67 " pdb=" N PHE D 67 " pdb=" C PHE D 67 " pdb=" CB PHE D 67 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CG LEU B 945 " pdb=" CB LEU B 945 " pdb=" CD1 LEU B 945 " pdb=" CD2 LEU B 945 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE C 203 " pdb=" N ILE C 203 " pdb=" C ILE C 203 " pdb=" CB ILE C 203 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 3628 not shown) Planarity restraints: 4115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 954 " 0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C GLN B 954 " -0.066 2.00e-02 2.50e+03 pdb=" O GLN B 954 " 0.025 2.00e-02 2.50e+03 pdb=" N ASN B 955 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C1098 " -0.019 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" C ASN C1098 " 0.066 2.00e-02 2.50e+03 pdb=" O ASN C1098 " -0.025 2.00e-02 2.50e+03 pdb=" N GLY C1099 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 948 " 0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C LEU A 948 " -0.064 2.00e-02 2.50e+03 pdb=" O LEU A 948 " 0.024 2.00e-02 2.50e+03 pdb=" N GLN A 949 " 0.022 2.00e-02 2.50e+03 ... (remaining 4112 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 275 2.65 - 3.21: 20001 3.21 - 3.77: 34691 3.77 - 4.34: 49382 4.34 - 4.90: 81618 Nonbonded interactions: 185967 Sorted by model distance: nonbonded pdb=" O THR C 108 " pdb=" OG1 THR C 236 " model vdw 2.083 3.040 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 158 " model vdw 2.161 3.120 nonbonded pdb=" NZ LYS B1028 " pdb=" O PHE B1042 " model vdw 2.252 3.120 nonbonded pdb=" OG1 THR A 33 " pdb=" O GLY A 219 " model vdw 2.274 3.040 nonbonded pdb=" OG1 THR C1077 " pdb=" O PHE C1095 " model vdw 2.293 3.040 ... (remaining 185962 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 'B' and (resid 28 through 1144 or resid 1301 through 1303)) selection = (chain 'C' and (resid 28 through 143 or resid 154 through 331 or resid 531 throu \ gh 1144 or resid 1302 through 1304)) } ncs_group { reference = (chain 'D' and (resid 2 through 33 or resid 35 through 94 or resid 99 or resid 1 \ 00C or resid 100F or resid 100H through 112)) selection = (chain 'H' and (resid 2 through 33 or resid 35 through 94 or resid 99 or resid 1 \ 00C or resid 100F or resid 100J through 112)) } 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: 3.830 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: 0.010 Extract box with map and model: 0.840 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 52.910 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.130 23355 Z= 0.248 Angle : 1.043 53.787 31813 Z= 0.599 Chirality : 0.056 0.223 3631 Planarity : 0.006 0.039 4102 Dihedral : 10.603 87.138 8554 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.20 % Allowed : 1.06 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.14), residues: 2844 helix: 1.11 (0.19), residues: 603 sheet: 1.06 (0.20), residues: 628 loop : -0.00 (0.14), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP H 47 HIS 0.009 0.002 HIS B 655 PHE 0.031 0.002 PHE B 133 TYR 0.047 0.003 TYR H 100D ARG 0.009 0.001 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 13) link_NAG-ASN : angle 2.15956 ( 39) hydrogen bonds : bond 0.13236 ( 997) hydrogen bonds : angle 7.63291 ( 2841) SS BOND : bond 0.02216 ( 37) SS BOND : angle 7.70451 ( 74) covalent geometry : bond 0.00550 (23305) covalent geometry : angle 0.97387 (31700) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 464 time to evaluate : 2.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.5993 (mt) cc_final: 0.5172 (tp) REVERT: A 153 MET cc_start: 0.2745 (tpt) cc_final: 0.2174 (ptp) REVERT: A 558 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7596 (ptpt) REVERT: A 581 THR cc_start: 0.8104 (m) cc_final: 0.7878 (p) REVERT: H 32 TYR cc_start: 0.4590 (m-80) cc_final: 0.4105 (m-10) REVERT: H 37 TYR cc_start: 0.5515 (t80) cc_final: 0.4945 (t80) REVERT: H 58 TYR cc_start: 0.7677 (t80) cc_final: 0.7438 (t80) REVERT: H 89 VAL cc_start: 0.7162 (t) cc_final: 0.6709 (p) REVERT: D 36 TRP cc_start: 0.7023 (m100) cc_final: 0.5629 (m100) REVERT: D 37 TYR cc_start: 0.7727 (m-80) cc_final: 0.7489 (m-80) REVERT: D 71 ARG cc_start: 0.6846 (ppt90) cc_final: 0.6416 (ptt90) REVERT: D 78 LEU cc_start: 0.7706 (tp) cc_final: 0.5926 (tp) REVERT: D 80 LEU cc_start: 0.7754 (tt) cc_final: 0.7029 (tt) REVERT: C 153 MET cc_start: 0.5757 (mmm) cc_final: 0.4588 (ttt) REVERT: C 190 ARG cc_start: 0.5692 (mtm-85) cc_final: 0.5489 (tpp80) REVERT: C 539 VAL cc_start: 0.8190 (t) cc_final: 0.7894 (p) REVERT: C 646 ARG cc_start: 0.7243 (tpt90) cc_final: 0.6659 (tpt90) REVERT: C 856 ASN cc_start: 0.7230 (m-40) cc_final: 0.6921 (p0) REVERT: B 761 THR cc_start: 0.8528 (m) cc_final: 0.8303 (p) REVERT: B 1029 MET cc_start: 0.8891 (tpp) cc_final: 0.8595 (tpp) outliers start: 5 outliers final: 3 residues processed: 467 average time/residue: 0.4296 time to fit residues: 301.1725 Evaluate side-chains 212 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 209 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 242 optimal weight: 6.9990 chunk 217 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 146 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 224 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 167 optimal weight: 0.7980 chunk 260 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN A 955 ASN H 39 GLN H 82AASN C 245 HIS C 532 ASN C 655 HIS C 926 GLN C 935 GLN C 955 ASN C1010 GLN C1101 HIS B 81 ASN B 165 ASN B 188 ASN B 239 GLN B 655 HIS B1048 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.108442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.073796 restraints weight = 52926.198| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.29 r_work: 0.2947 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.139 23355 Z= 0.223 Angle : 0.659 13.209 31813 Z= 0.351 Chirality : 0.047 0.320 3631 Planarity : 0.005 0.059 4102 Dihedral : 5.284 59.417 3374 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.77 % Allowed : 5.04 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.15), residues: 2844 helix: 2.47 (0.20), residues: 607 sheet: 0.93 (0.19), residues: 651 loop : -0.30 (0.14), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 353 HIS 0.007 0.002 HIS B 655 PHE 0.020 0.002 PHE B 133 TYR 0.031 0.002 TYR H 37 ARG 0.006 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 13) link_NAG-ASN : angle 2.15330 ( 39) hydrogen bonds : bond 0.05024 ( 997) hydrogen bonds : angle 6.00065 ( 2841) SS BOND : bond 0.00911 ( 37) SS BOND : angle 1.68785 ( 74) covalent geometry : bond 0.00517 (23305) covalent geometry : angle 0.65061 (31700) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.5430 (p90) cc_final: 0.5145 (p90) REVERT: A 141 LEU cc_start: 0.5892 (mt) cc_final: 0.5506 (tp) REVERT: A 153 MET cc_start: 0.2565 (tpt) cc_final: 0.2128 (ptp) REVERT: A 271 GLN cc_start: 0.7879 (mp10) cc_final: 0.7676 (mp10) REVERT: A 558 LYS cc_start: 0.8149 (mmtt) cc_final: 0.7742 (ptpt) REVERT: H 59 TYR cc_start: 0.6515 (m-80) cc_final: 0.5994 (m-80) REVERT: H 100 ARG cc_start: 0.7410 (mpp-170) cc_final: 0.7051 (mpp80) REVERT: D 36 TRP cc_start: 0.7012 (m100) cc_final: 0.6753 (m100) REVERT: D 43 LYS cc_start: 0.6884 (mppt) cc_final: 0.6535 (mmmt) REVERT: D 81 GLN cc_start: 0.7318 (tm-30) cc_final: 0.6739 (tm-30) REVERT: D 100 PHE cc_start: 0.8034 (m-10) cc_final: 0.7435 (m-10) REVERT: C 131 CYS cc_start: 0.4225 (OUTLIER) cc_final: 0.3441 (m) REVERT: C 153 MET cc_start: 0.5803 (mmm) cc_final: 0.4585 (ttt) REVERT: C 190 ARG cc_start: 0.5864 (mtm-85) cc_final: 0.5387 (tpp80) REVERT: C 546 LEU cc_start: 0.7129 (tp) cc_final: 0.6740 (mm) REVERT: C 646 ARG cc_start: 0.7735 (tpt90) cc_final: 0.7091 (tpt90) REVERT: C 856 ASN cc_start: 0.7266 (m-40) cc_final: 0.7052 (p0) REVERT: B 115 GLN cc_start: 0.7389 (mt0) cc_final: 0.7049 (mm-40) outliers start: 45 outliers final: 26 residues processed: 254 average time/residue: 0.3566 time to fit residues: 141.6829 Evaluate side-chains 198 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 988 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 260 optimal weight: 0.6980 chunk 286 optimal weight: 8.9990 chunk 254 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 244 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 28 optimal weight: 8.9990 chunk 234 optimal weight: 6.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS D 73 ASN D 76 ASN C 81 ASN C 901 GLN C1074 ASN B 81 ASN B 901 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.107335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.072480 restraints weight = 52632.370| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.24 r_work: 0.2932 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 23355 Z= 0.200 Angle : 0.601 9.606 31813 Z= 0.317 Chirality : 0.046 0.262 3631 Planarity : 0.004 0.054 4102 Dihedral : 4.994 50.337 3372 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.60 % Favored : 97.36 % Rotamer: Outliers : 1.97 % Allowed : 6.97 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 2844 helix: 2.77 (0.20), residues: 608 sheet: 0.78 (0.19), residues: 653 loop : -0.55 (0.14), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 36 HIS 0.006 0.001 HIS B1058 PHE 0.020 0.002 PHE B 133 TYR 0.023 0.002 TYR H 100F ARG 0.006 0.001 ARG D 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 13) link_NAG-ASN : angle 2.12303 ( 39) hydrogen bonds : bond 0.04735 ( 997) hydrogen bonds : angle 5.73913 ( 2841) SS BOND : bond 0.00633 ( 37) SS BOND : angle 1.55522 ( 74) covalent geometry : bond 0.00469 (23305) covalent geometry : angle 0.59242 (31700) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 194 time to evaluate : 2.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.5064 (t0) cc_final: 0.4750 (t0) REVERT: A 141 LEU cc_start: 0.6059 (mt) cc_final: 0.5326 (tp) REVERT: A 153 MET cc_start: 0.3124 (tpt) cc_final: 0.2366 (ptp) REVERT: A 168 PHE cc_start: 0.4806 (t80) cc_final: 0.4601 (t80) REVERT: A 558 LYS cc_start: 0.8210 (mmtt) cc_final: 0.7793 (ptpt) REVERT: H 58 TYR cc_start: 0.8006 (t80) cc_final: 0.7400 (t80) REVERT: H 59 TYR cc_start: 0.6635 (m-80) cc_final: 0.6280 (m-80) REVERT: H 89 VAL cc_start: 0.7514 (t) cc_final: 0.7179 (p) REVERT: H 100 ARG cc_start: 0.7441 (mpp-170) cc_final: 0.7107 (mpp80) REVERT: D 37 TYR cc_start: 0.8086 (m-80) cc_final: 0.7616 (m-80) REVERT: D 43 LYS cc_start: 0.6996 (mppt) cc_final: 0.6782 (mmtt) REVERT: C 81 ASN cc_start: 0.6587 (t0) cc_final: 0.6295 (t0) REVERT: C 131 CYS cc_start: 0.4154 (OUTLIER) cc_final: 0.3327 (m) REVERT: C 153 MET cc_start: 0.5800 (mmm) cc_final: 0.4703 (ttt) REVERT: C 190 ARG cc_start: 0.5939 (mtm-85) cc_final: 0.5260 (ttm-80) REVERT: C 266 TYR cc_start: 0.6955 (m-80) cc_final: 0.6705 (m-80) REVERT: C 646 ARG cc_start: 0.7739 (tpt90) cc_final: 0.7068 (tpt90) REVERT: B 115 GLN cc_start: 0.7531 (mt0) cc_final: 0.7064 (mm-40) REVERT: B 795 LYS cc_start: 0.6375 (mmtm) cc_final: 0.6152 (mmtm) outliers start: 50 outliers final: 30 residues processed: 231 average time/residue: 0.3538 time to fit residues: 127.8027 Evaluate side-chains 190 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 984 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 156 optimal weight: 9.9990 chunk 204 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 247 optimal weight: 0.4980 chunk 242 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 264 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1074 ASN B 239 GLN B 955 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.106405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.072812 restraints weight = 53197.024| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.26 r_work: 0.2903 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 23355 Z= 0.198 Angle : 0.586 13.053 31813 Z= 0.307 Chirality : 0.045 0.269 3631 Planarity : 0.004 0.044 4102 Dihedral : 4.924 40.599 3372 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.46 % Favored : 97.50 % Rotamer: Outliers : 2.13 % Allowed : 7.21 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.15), residues: 2844 helix: 2.98 (0.20), residues: 598 sheet: 0.65 (0.19), residues: 675 loop : -0.65 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 36 HIS 0.007 0.001 HIS B1058 PHE 0.020 0.002 PHE B 898 TYR 0.024 0.002 TYR H 100F ARG 0.005 0.001 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 13) link_NAG-ASN : angle 2.14658 ( 39) hydrogen bonds : bond 0.04578 ( 997) hydrogen bonds : angle 5.64469 ( 2841) SS BOND : bond 0.00646 ( 37) SS BOND : angle 1.46132 ( 74) covalent geometry : bond 0.00467 (23305) covalent geometry : angle 0.57779 (31700) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 189 time to evaluate : 2.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.5019 (t0) cc_final: 0.4688 (t0) REVERT: A 141 LEU cc_start: 0.6113 (mt) cc_final: 0.5344 (tp) REVERT: A 153 MET cc_start: 0.3301 (tpt) cc_final: 0.2375 (ptp) REVERT: A 168 PHE cc_start: 0.4812 (t80) cc_final: 0.4582 (t80) REVERT: A 271 GLN cc_start: 0.7807 (mp10) cc_final: 0.7568 (mp10) REVERT: A 273 ARG cc_start: 0.7967 (mmm-85) cc_final: 0.7537 (mmm-85) REVERT: A 400 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.8203 (p90) REVERT: A 558 LYS cc_start: 0.8266 (mmtt) cc_final: 0.7848 (ptpt) REVERT: A 613 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7602 (mp10) REVERT: H 58 TYR cc_start: 0.7869 (t80) cc_final: 0.7259 (t80) REVERT: H 59 TYR cc_start: 0.6897 (m-80) cc_final: 0.6396 (m-80) REVERT: H 89 VAL cc_start: 0.7565 (t) cc_final: 0.7029 (p) REVERT: H 100 ARG cc_start: 0.7696 (mpp-170) cc_final: 0.7323 (mpp80) REVERT: D 37 TYR cc_start: 0.8105 (m-80) cc_final: 0.7572 (m-80) REVERT: D 43 LYS cc_start: 0.7022 (mppt) cc_final: 0.6652 (mmmm) REVERT: D 75 LYS cc_start: 0.8253 (mmmt) cc_final: 0.8026 (tptp) REVERT: C 81 ASN cc_start: 0.6566 (t0) cc_final: 0.6278 (t0) REVERT: C 131 CYS cc_start: 0.3946 (OUTLIER) cc_final: 0.3189 (m) REVERT: C 153 MET cc_start: 0.5812 (mmm) cc_final: 0.4715 (ttt) REVERT: C 190 ARG cc_start: 0.5629 (mtm-85) cc_final: 0.5306 (mtm-85) REVERT: C 266 TYR cc_start: 0.6966 (m-80) cc_final: 0.6302 (m-80) REVERT: C 646 ARG cc_start: 0.7795 (tpt90) cc_final: 0.7136 (tpt90) REVERT: B 115 GLN cc_start: 0.7399 (mt0) cc_final: 0.7024 (mm-40) REVERT: B 795 LYS cc_start: 0.6375 (mmtm) cc_final: 0.6126 (mmtm) REVERT: B 1138 TYR cc_start: 0.8708 (t80) cc_final: 0.8477 (t80) outliers start: 54 outliers final: 40 residues processed: 228 average time/residue: 0.3567 time to fit residues: 127.4112 Evaluate side-chains 209 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 166 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 201 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 200 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS D 73 ASN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 787 GLN C1074 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.108010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.073591 restraints weight = 53350.826| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.38 r_work: 0.2950 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 23355 Z= 0.115 Angle : 0.519 12.692 31813 Z= 0.272 Chirality : 0.043 0.253 3631 Planarity : 0.004 0.057 4102 Dihedral : 4.526 35.391 3372 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.29 % Favored : 97.68 % Rotamer: Outliers : 1.58 % Allowed : 8.04 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.15), residues: 2844 helix: 3.25 (0.20), residues: 599 sheet: 0.70 (0.19), residues: 653 loop : -0.63 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 36 HIS 0.003 0.001 HIS A 207 PHE 0.019 0.001 PHE D 67 TYR 0.023 0.001 TYR H 100F ARG 0.007 0.000 ARG D 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 13) link_NAG-ASN : angle 1.90581 ( 39) hydrogen bonds : bond 0.03898 ( 997) hydrogen bonds : angle 5.30831 ( 2841) SS BOND : bond 0.00512 ( 37) SS BOND : angle 1.32254 ( 74) covalent geometry : bond 0.00260 (23305) covalent geometry : angle 0.51184 (31700) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 2.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.4978 (t0) cc_final: 0.4635 (t0) REVERT: A 141 LEU cc_start: 0.5972 (mt) cc_final: 0.5252 (tp) REVERT: A 153 MET cc_start: 0.3100 (tpt) cc_final: 0.2256 (ptp) REVERT: A 273 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.7289 (mmm-85) REVERT: A 400 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8356 (p90) REVERT: A 558 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7828 (ptpt) REVERT: A 599 THR cc_start: 0.9368 (OUTLIER) cc_final: 0.9034 (p) REVERT: A 950 ASP cc_start: 0.8667 (t0) cc_final: 0.8402 (t0) REVERT: H 58 TYR cc_start: 0.7798 (t80) cc_final: 0.7225 (t80) REVERT: H 59 TYR cc_start: 0.7006 (m-80) cc_final: 0.6349 (m-80) REVERT: H 89 VAL cc_start: 0.7413 (t) cc_final: 0.7097 (p) REVERT: H 100 ARG cc_start: 0.7899 (mpp-170) cc_final: 0.7576 (mpp80) REVERT: H 103 TRP cc_start: 0.6748 (OUTLIER) cc_final: 0.5905 (m-90) REVERT: D 37 TYR cc_start: 0.8139 (m-80) cc_final: 0.7568 (m-80) REVERT: D 43 LYS cc_start: 0.7154 (mppt) cc_final: 0.6920 (mmmm) REVERT: D 47 TRP cc_start: 0.7838 (t60) cc_final: 0.7591 (t60) REVERT: D 75 LYS cc_start: 0.8251 (mmmt) cc_final: 0.7997 (tptp) REVERT: D 102 TYR cc_start: 0.8756 (m-80) cc_final: 0.8388 (m-80) REVERT: D 103 TRP cc_start: 0.7330 (m100) cc_final: 0.6579 (m100) REVERT: C 81 ASN cc_start: 0.6418 (t0) cc_final: 0.6161 (t0) REVERT: C 131 CYS cc_start: 0.4049 (OUTLIER) cc_final: 0.3368 (m) REVERT: C 153 MET cc_start: 0.5802 (mmm) cc_final: 0.4739 (ttt) REVERT: C 190 ARG cc_start: 0.5614 (mtm-85) cc_final: 0.5292 (mtm-85) REVERT: C 266 TYR cc_start: 0.6952 (m-80) cc_final: 0.6338 (m-80) REVERT: C 646 ARG cc_start: 0.7759 (tpt90) cc_final: 0.7075 (tpt90) REVERT: B 115 GLN cc_start: 0.7444 (mt0) cc_final: 0.7006 (mm-40) outliers start: 40 outliers final: 23 residues processed: 223 average time/residue: 0.3540 time to fit residues: 124.6396 Evaluate side-chains 200 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 168 optimal weight: 3.9990 chunk 238 optimal weight: 0.5980 chunk 51 optimal weight: 7.9990 chunk 103 optimal weight: 20.0000 chunk 235 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 262 optimal weight: 0.0170 chunk 161 optimal weight: 7.9990 chunk 199 optimal weight: 0.6980 chunk 231 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 overall best weight: 2.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS H 97 GLN D 73 ASN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1074 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.106475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.072080 restraints weight = 53090.074| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.21 r_work: 0.2921 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23355 Z= 0.183 Angle : 0.562 12.172 31813 Z= 0.292 Chirality : 0.044 0.253 3631 Planarity : 0.004 0.056 4102 Dihedral : 4.599 35.289 3370 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.71 % Favored : 97.26 % Rotamer: Outliers : 2.05 % Allowed : 8.55 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.15), residues: 2844 helix: 2.92 (0.20), residues: 620 sheet: 0.69 (0.19), residues: 669 loop : -0.69 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 64 HIS 0.010 0.001 HIS A 207 PHE 0.019 0.001 PHE D 67 TYR 0.025 0.001 TYR H 100F ARG 0.005 0.000 ARG H 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 13) link_NAG-ASN : angle 2.00752 ( 39) hydrogen bonds : bond 0.04291 ( 997) hydrogen bonds : angle 5.40107 ( 2841) SS BOND : bond 0.00609 ( 37) SS BOND : angle 1.83392 ( 74) covalent geometry : bond 0.00431 (23305) covalent geometry : angle 0.55100 (31700) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 178 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.5018 (t0) cc_final: 0.4735 (t0) REVERT: A 558 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7887 (ptpt) REVERT: A 613 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7560 (mp10) REVERT: A 950 ASP cc_start: 0.8614 (t0) cc_final: 0.8307 (t0) REVERT: H 45 ARG cc_start: 0.7804 (mmp80) cc_final: 0.7526 (mmp80) REVERT: H 58 TYR cc_start: 0.7777 (t80) cc_final: 0.7313 (t80) REVERT: H 59 TYR cc_start: 0.7020 (m-80) cc_final: 0.6322 (m-80) REVERT: H 89 VAL cc_start: 0.7524 (t) cc_final: 0.7282 (p) REVERT: H 96 TYR cc_start: 0.7190 (t80) cc_final: 0.6816 (t80) REVERT: H 100 ASP cc_start: 0.7090 (m-30) cc_final: 0.6861 (m-30) REVERT: H 103 TRP cc_start: 0.6654 (OUTLIER) cc_final: 0.5931 (m-90) REVERT: D 37 TYR cc_start: 0.8056 (m-80) cc_final: 0.7606 (m-80) REVERT: D 75 LYS cc_start: 0.8220 (mmmt) cc_final: 0.8010 (tptp) REVERT: D 101 ASP cc_start: 0.7915 (m-30) cc_final: 0.7630 (m-30) REVERT: D 103 TRP cc_start: 0.7465 (m100) cc_final: 0.6287 (m100) REVERT: C 81 ASN cc_start: 0.6394 (t0) cc_final: 0.6165 (t0) REVERT: C 131 CYS cc_start: 0.3938 (OUTLIER) cc_final: 0.3097 (m) REVERT: C 153 MET cc_start: 0.5830 (mmm) cc_final: 0.4775 (ttt) REVERT: C 157 PHE cc_start: 0.5656 (OUTLIER) cc_final: 0.5335 (m-80) REVERT: C 190 ARG cc_start: 0.5701 (mtm-85) cc_final: 0.5308 (mtm-85) REVERT: C 207 HIS cc_start: 0.5605 (t-170) cc_final: 0.5340 (p-80) REVERT: C 646 ARG cc_start: 0.7771 (tpt90) cc_final: 0.7090 (tpt90) REVERT: B 115 GLN cc_start: 0.7430 (mt0) cc_final: 0.7065 (mm-40) outliers start: 52 outliers final: 42 residues processed: 215 average time/residue: 0.3424 time to fit residues: 115.5510 Evaluate side-chains 209 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 163 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1081 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 112 optimal weight: 0.8980 chunk 128 optimal weight: 7.9990 chunk 200 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 251 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 184 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 257 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1074 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.106914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.073121 restraints weight = 52965.838| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.28 r_work: 0.2924 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 23355 Z= 0.138 Angle : 0.533 11.297 31813 Z= 0.277 Chirality : 0.043 0.244 3631 Planarity : 0.004 0.056 4102 Dihedral : 4.477 35.902 3368 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.64 % Favored : 97.33 % Rotamer: Outliers : 2.01 % Allowed : 8.55 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.15), residues: 2844 helix: 3.06 (0.20), residues: 613 sheet: 0.70 (0.20), residues: 655 loop : -0.64 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 64 HIS 0.004 0.001 HIS B1058 PHE 0.018 0.001 PHE D 67 TYR 0.025 0.001 TYR H 100F ARG 0.005 0.000 ARG D 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 13) link_NAG-ASN : angle 1.90480 ( 39) hydrogen bonds : bond 0.03988 ( 997) hydrogen bonds : angle 5.27796 ( 2841) SS BOND : bond 0.00548 ( 37) SS BOND : angle 1.70726 ( 74) covalent geometry : bond 0.00324 (23305) covalent geometry : angle 0.52364 (31700) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 179 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.5069 (t0) cc_final: 0.4797 (t0) REVERT: A 160 TYR cc_start: 0.4720 (m-80) cc_final: 0.4414 (m-80) REVERT: A 558 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7924 (ptpt) REVERT: A 613 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7559 (mp10) REVERT: H 58 TYR cc_start: 0.7824 (t80) cc_final: 0.7413 (t80) REVERT: H 59 TYR cc_start: 0.6946 (m-80) cc_final: 0.6222 (m-80) REVERT: H 89 VAL cc_start: 0.7554 (t) cc_final: 0.7177 (p) REVERT: H 96 TYR cc_start: 0.7304 (t80) cc_final: 0.7072 (t80) REVERT: H 100 ASP cc_start: 0.7248 (m-30) cc_final: 0.7026 (m-30) REVERT: D 37 TYR cc_start: 0.8045 (m-80) cc_final: 0.7396 (m-80) REVERT: D 101 ASP cc_start: 0.7853 (m-30) cc_final: 0.7515 (m-30) REVERT: C 131 CYS cc_start: 0.3910 (OUTLIER) cc_final: 0.3163 (m) REVERT: C 153 MET cc_start: 0.5825 (mmm) cc_final: 0.4763 (ttt) REVERT: C 157 PHE cc_start: 0.5754 (OUTLIER) cc_final: 0.5487 (m-80) REVERT: C 190 ARG cc_start: 0.5706 (mtm-85) cc_final: 0.5317 (mtm-85) REVERT: C 207 HIS cc_start: 0.5515 (t-170) cc_final: 0.5282 (p-80) REVERT: C 266 TYR cc_start: 0.6954 (m-80) cc_final: 0.6248 (m-80) REVERT: C 646 ARG cc_start: 0.7789 (tpt90) cc_final: 0.7119 (tpt90) REVERT: B 115 GLN cc_start: 0.7457 (mt0) cc_final: 0.7073 (mm-40) outliers start: 51 outliers final: 41 residues processed: 215 average time/residue: 0.3522 time to fit residues: 120.8911 Evaluate side-chains 203 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1081 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 23 optimal weight: 0.0670 chunk 242 optimal weight: 0.7980 chunk 165 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 143 optimal weight: 20.0000 chunk 215 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 152 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1074 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.106284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.073114 restraints weight = 52908.882| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.22 r_work: 0.2910 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 23355 Z= 0.171 Angle : 0.548 12.778 31813 Z= 0.285 Chirality : 0.044 0.252 3631 Planarity : 0.004 0.062 4102 Dihedral : 4.548 35.772 3368 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.16 % Favored : 96.80 % Rotamer: Outliers : 2.36 % Allowed : 8.31 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.15), residues: 2844 helix: 3.02 (0.20), residues: 613 sheet: 0.68 (0.20), residues: 643 loop : -0.68 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 64 HIS 0.006 0.001 HIS B1058 PHE 0.023 0.001 PHE C 135 TYR 0.025 0.001 TYR H 100F ARG 0.004 0.000 ARG D 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 13) link_NAG-ASN : angle 1.97714 ( 39) hydrogen bonds : bond 0.04171 ( 997) hydrogen bonds : angle 5.32049 ( 2841) SS BOND : bond 0.00593 ( 37) SS BOND : angle 1.47701 ( 74) covalent geometry : bond 0.00405 (23305) covalent geometry : angle 0.53960 (31700) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 161 time to evaluate : 3.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3130 (ttp) cc_final: 0.2896 (mtp) REVERT: A 160 TYR cc_start: 0.4652 (m-80) cc_final: 0.4309 (m-80) REVERT: A 558 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7877 (ptpt) REVERT: A 613 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7600 (mp10) REVERT: H 37 TYR cc_start: 0.6399 (OUTLIER) cc_final: 0.6124 (t80) REVERT: H 48 VAL cc_start: 0.7922 (t) cc_final: 0.7651 (t) REVERT: H 59 TYR cc_start: 0.6877 (m-80) cc_final: 0.6269 (m-80) REVERT: H 89 VAL cc_start: 0.7550 (t) cc_final: 0.7312 (p) REVERT: H 96 TYR cc_start: 0.7340 (t80) cc_final: 0.7052 (t80) REVERT: H 100 ASP cc_start: 0.7237 (m-30) cc_final: 0.7011 (m-30) REVERT: H 103 TRP cc_start: 0.6645 (OUTLIER) cc_final: 0.5960 (m-90) REVERT: D 100 THR cc_start: 0.8384 (p) cc_final: 0.8040 (t) REVERT: C 131 CYS cc_start: 0.3908 (OUTLIER) cc_final: 0.3148 (m) REVERT: C 153 MET cc_start: 0.5858 (mmm) cc_final: 0.4788 (ttt) REVERT: C 157 PHE cc_start: 0.5800 (OUTLIER) cc_final: 0.5533 (m-80) REVERT: C 190 ARG cc_start: 0.5734 (mtm-85) cc_final: 0.5289 (mtm-85) REVERT: C 646 ARG cc_start: 0.7800 (tpt90) cc_final: 0.7110 (tpt90) REVERT: B 115 GLN cc_start: 0.7432 (mt0) cc_final: 0.7078 (mm-40) REVERT: B 900 MET cc_start: 0.8994 (mtp) cc_final: 0.8787 (mtp) outliers start: 60 outliers final: 50 residues processed: 205 average time/residue: 0.3378 time to fit residues: 110.9870 Evaluate side-chains 205 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 150 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1081 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.4421 > 50: distance: 100 - 166: 8.604 distance: 114 - 153: 20.308 distance: 117 - 150: 20.680 distance: 133 - 137: 12.900 distance: 137 - 138: 5.147 distance: 138 - 139: 16.016 distance: 138 - 141: 9.571 distance: 139 - 140: 12.093 distance: 139 - 142: 10.663 distance: 142 - 143: 11.651 distance: 143 - 144: 14.499 distance: 143 - 146: 18.816 distance: 144 - 145: 13.979 distance: 144 - 150: 23.488 distance: 146 - 147: 18.806 distance: 147 - 148: 7.622 distance: 147 - 149: 6.478 distance: 150 - 151: 7.261 distance: 151 - 152: 15.596 distance: 151 - 154: 23.608 distance: 152 - 153: 22.246 distance: 152 - 159: 27.859 distance: 154 - 155: 13.216 distance: 155 - 156: 25.885 distance: 156 - 157: 8.755 distance: 156 - 158: 31.740 distance: 159 - 160: 3.825 distance: 159 - 165: 9.896 distance: 160 - 161: 12.559 distance: 160 - 163: 16.346 distance: 161 - 162: 11.666 distance: 161 - 166: 12.101 distance: 163 - 164: 16.686 distance: 164 - 165: 21.028 distance: 166 - 167: 7.724 distance: 167 - 168: 11.733 distance: 167 - 170: 14.767 distance: 168 - 169: 15.007 distance: 168 - 174: 8.830 distance: 170 - 171: 5.169 distance: 171 - 172: 8.897 distance: 171 - 173: 14.135 distance: 174 - 175: 12.283 distance: 175 - 176: 9.135 distance: 175 - 178: 16.784 distance: 176 - 177: 9.179 distance: 176 - 181: 9.390 distance: 178 - 179: 15.329 distance: 178 - 180: 17.332 distance: 181 - 182: 7.052 distance: 182 - 183: 12.998 distance: 182 - 185: 5.400 distance: 183 - 184: 17.360 distance: 183 - 189: 9.399 distance: 185 - 186: 7.597 distance: 186 - 187: 5.692 distance: 186 - 188: 12.362 distance: 189 - 190: 4.899 distance: 190 - 191: 5.434 distance: 190 - 193: 4.640 distance: 191 - 192: 21.594 distance: 191 - 197: 17.556 distance: 193 - 194: 8.944 distance: 194 - 195: 12.771 distance: 194 - 196: 25.922 distance: 197 - 198: 12.459 distance: 197 - 203: 7.541 distance: 198 - 199: 8.723 distance: 198 - 201: 6.794 distance: 199 - 200: 7.191 distance: 199 - 204: 15.822 distance: 201 - 202: 17.825 distance: 202 - 203: 15.982 distance: 204 - 205: 7.058 distance: 205 - 206: 3.633 distance: 206 - 207: 10.675 distance: 206 - 212: 5.575 distance: 208 - 209: 10.513 distance: 208 - 210: 14.608 distance: 209 - 211: 16.697