Starting phenix.real_space_refine on Fri May 23 09:31:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lwj_23547/05_2025/7lwj_23547.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lwj_23547/05_2025/7lwj_23547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lwj_23547/05_2025/7lwj_23547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lwj_23547/05_2025/7lwj_23547.map" model { file = "/net/cci-nas-00/data/ceres_data/7lwj_23547/05_2025/7lwj_23547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lwj_23547/05_2025/7lwj_23547.cif" } resolution = 3.24 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= -0.001 sd= 0.057 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 98 5.16 5 C 15204 2.51 5 N 3924 2.21 5 O 4614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 23840 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7807 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 7807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7807 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "C" Number of atoms: 7806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7806 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 13.28, per 1000 atoms: 0.56 Number of scatterers: 23840 At special positions: 0 Unit cell: (130.418, 136.832, 167.833, 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 98 16.00 O 4614 8.00 N 3924 7.00 C 15204 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.06 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.01 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A 165 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 122 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 165 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C 122 " Time building additional restraints: 5.86 Conformation dependent library (CDL) restraints added in 3.0 seconds 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5622 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 51 sheets defined 27.1% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.17 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.900A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.825A 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 438 through 443 removed outlier: 3.838A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 754 through 757 Processing helix chain 'A' and resid 758 through 782 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 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 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: 3.953A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.735A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.014A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.540A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 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 908 removed outlier: 3.610A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.625A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 941 through 944 Processing helix chain 'B' and resid 945 through 965 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 982 removed outlier: 3.850A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 1033 Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.525A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.584A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.787A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.771A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 756 removed outlier: 4.510A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.538A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.064A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) 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 891 removed outlier: 3.719A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.683A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.558A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (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 removed outlier: 3.989A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 986 through 1033 removed outlier: 3.792A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.047A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.021A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY A 89 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.625A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.194A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 317 removed outlier: 4.123A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.422A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 334 through 335 removed outlier: 6.711A pdb=" N ASN A 334 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 358 removed outlier: 4.718A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.829A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.349A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.322A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 4.423A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.531A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 65 through 66 removed outlier: 3.652A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.516A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.360A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 327 removed outlier: 6.937A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.826A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.922A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 656 removed outlier: 5.860A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.569A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 722 removed outlier: 6.961A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 725 through 728 Processing sheet with id=AD7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.605A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.603A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.801A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.848A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 141 through 142 removed outlier: 6.083A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.517A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.532A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.282A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 656 removed outlier: 4.632A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 719 removed outlier: 6.892A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 722 through 728 removed outlier: 3.721A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.430A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.367A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1011 hydrogen bonds defined for protein. 2718 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: 12.36 Time building geometry restraints manager: 6.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5580 1.33 - 1.45: 5229 1.45 - 1.58: 13428 1.58 - 1.70: 0 1.70 - 1.82: 122 Bond restraints: 24359 Sorted by residual: bond pdb=" CA PRO C 862 " pdb=" C PRO C 862 " ideal model delta sigma weight residual 1.514 1.536 -0.022 5.50e-03 3.31e+04 1.56e+01 bond pdb=" C5 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.413 1.492 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C5 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C5 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C5 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 24354 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 21828 1.69 - 3.38: 9038 3.38 - 5.06: 2020 5.06 - 6.75: 233 6.75 - 8.44: 18 Bond angle restraints: 33137 Sorted by residual: angle pdb=" CA PHE C 275 " pdb=" CB PHE C 275 " pdb=" CG PHE C 275 " ideal model delta sigma weight residual 113.80 120.63 -6.83 1.00e+00 1.00e+00 4.67e+01 angle pdb=" C GLY C 594 " pdb=" N VAL C 595 " pdb=" CA VAL C 595 " ideal model delta sigma weight residual 121.65 127.42 -5.77 9.40e-01 1.13e+00 3.76e+01 angle pdb=" CA PHE B 59 " pdb=" CB PHE B 59 " pdb=" CG PHE B 59 " ideal model delta sigma weight residual 113.80 119.66 -5.86 1.00e+00 1.00e+00 3.43e+01 angle pdb=" C GLY C 381 " pdb=" N VAL C 382 " pdb=" CA VAL C 382 " ideal model delta sigma weight residual 122.51 130.09 -7.58 1.31e+00 5.83e-01 3.35e+01 angle pdb=" CA PHE A 515 " pdb=" CB PHE A 515 " pdb=" CG PHE A 515 " ideal model delta sigma weight residual 113.80 119.49 -5.69 1.00e+00 1.00e+00 3.24e+01 ... (remaining 33132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 13710 17.79 - 35.59: 939 35.59 - 53.38: 164 53.38 - 71.18: 43 71.18 - 88.97: 29 Dihedral angle restraints: 14885 sinusoidal: 6158 harmonic: 8727 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual 93.00 176.83 -83.83 1 1.00e+01 1.00e-02 8.57e+01 dihedral pdb=" CA THR B 95 " pdb=" C THR B 95 " pdb=" N GLU B 96 " pdb=" CA GLU B 96 " ideal model delta harmonic sigma weight residual -180.00 -149.97 -30.03 0 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" CA ASN C1135 " pdb=" C ASN C1135 " pdb=" N THR C1136 " pdb=" CA THR C1136 " ideal model delta harmonic sigma weight residual 180.00 150.02 29.98 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 14882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2548 0.097 - 0.193: 1184 0.193 - 0.290: 126 0.290 - 0.387: 16 0.387 - 0.483: 2 Chirality restraints: 3876 Sorted by residual: chirality pdb=" CA GLU A 773 " pdb=" N GLU A 773 " pdb=" C GLU A 773 " pdb=" CB GLU A 773 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.84e+00 chirality pdb=" CA GLU C 773 " pdb=" N GLU C 773 " pdb=" C GLU C 773 " pdb=" CB GLU C 773 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.21e+00 chirality pdb=" CA ASP B1041 " pdb=" N ASP B1041 " pdb=" C ASP B1041 " pdb=" CB ASP B1041 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 3873 not shown) Planarity restraints: 4281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 917 " 0.224 2.00e-02 2.50e+03 1.29e-01 3.34e+02 pdb=" CG TYR C 917 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR C 917 " -0.084 2.00e-02 2.50e+03 pdb=" CD2 TYR C 917 " -0.140 2.00e-02 2.50e+03 pdb=" CE1 TYR C 917 " -0.104 2.00e-02 2.50e+03 pdb=" CE2 TYR C 917 " -0.063 2.00e-02 2.50e+03 pdb=" CZ TYR C 917 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 917 " 0.201 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 917 " 0.221 2.00e-02 2.50e+03 1.27e-01 3.22e+02 pdb=" CG TYR B 917 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR B 917 " -0.089 2.00e-02 2.50e+03 pdb=" CD2 TYR B 917 " -0.133 2.00e-02 2.50e+03 pdb=" CE1 TYR B 917 " -0.101 2.00e-02 2.50e+03 pdb=" CE2 TYR B 917 " -0.064 2.00e-02 2.50e+03 pdb=" CZ TYR B 917 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 917 " 0.197 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 917 " 0.203 2.00e-02 2.50e+03 1.18e-01 2.78e+02 pdb=" CG TYR A 917 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 917 " -0.070 2.00e-02 2.50e+03 pdb=" CD2 TYR A 917 " -0.124 2.00e-02 2.50e+03 pdb=" CE1 TYR A 917 " -0.100 2.00e-02 2.50e+03 pdb=" CE2 TYR A 917 " -0.056 2.00e-02 2.50e+03 pdb=" CZ TYR A 917 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 917 " 0.187 2.00e-02 2.50e+03 ... (remaining 4278 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 10976 2.97 - 3.45: 23750 3.45 - 3.93: 40331 3.93 - 4.42: 45459 4.42 - 4.90: 76135 Nonbonded interactions: 196651 Sorted by model distance: nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.482 3.040 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.485 3.040 nonbonded pdb=" OH TYR A 200 " pdb=" OE2 GLU C 516 " model vdw 2.519 3.040 nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.523 3.040 nonbonded pdb=" OG SER C 813 " pdb=" OE1 GLU C 868 " model vdw 2.530 3.040 ... (remaining 196646 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 479 or (resid 480 and (name N or name CA or nam \ e C or name O or name CB )) or resid 481 through 487 or (resid 488 and (name N o \ r name CA or name C or name O or name CB )) or resid 489 through 589 or (resid 5 \ 90 and (name N or name CA or name C or name O or name CB )) or resid 591 through \ 1147 or resid 1301 through 1310)) selection = (chain 'B' and (resid 27 through 360 or (resid 361 and (name N or name CA or nam \ e C or name O or name CB )) or resid 362 through 390 or (resid 391 and (name N o \ r name CA or name C or name O or name CB )) or resid 392 through 589 or (resid 5 \ 90 and (name N or name CA or name C or name O or name CB )) or resid 591 through \ 1147 or resid 1301 through 1310)) selection = (chain 'C' and (resid 27 through 360 or (resid 361 and (name N or name CA or nam \ e C or name O or name CB )) or resid 362 through 390 or (resid 391 and (name N o \ r name CA or name C or name O or name CB )) or resid 392 through 1147 or resid 1 \ 301 through 1310)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 57.000 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.120 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 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 : 0.014 0.079 24423 Z= 0.799 Angle : 1.841 9.848 33295 Z= 1.228 Chirality : 0.098 0.483 3876 Planarity : 0.015 0.174 4251 Dihedral : 13.345 88.970 9161 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.01 % Favored : 92.79 % Rotamer: Outliers : 0.84 % Allowed : 3.21 % Favored : 95.95 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.14), residues: 2955 helix: -1.30 (0.17), residues: 665 sheet: -0.34 (0.25), residues: 357 loop : -1.34 (0.13), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.178 0.026 TRP B 886 HIS 0.017 0.003 HIS A1064 PHE 0.101 0.015 PHE A 718 TYR 0.224 0.026 TYR C 917 ARG 0.009 0.001 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.01180 ( 30) link_NAG-ASN : angle 4.45901 ( 90) hydrogen bonds : bond 0.13814 ( 1009) hydrogen bonds : angle 8.83184 ( 2718) SS BOND : bond 0.01090 ( 34) SS BOND : angle 2.28498 ( 68) covalent geometry : bond 0.01369 (24359) covalent geometry : angle 1.82768 (33137) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 358 time to evaluate : 2.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7445 (tp) cc_final: 0.7123 (pp) REVERT: A 347 PHE cc_start: 0.1688 (OUTLIER) cc_final: 0.1016 (t80) REVERT: B 38 TYR cc_start: 0.3781 (m-80) cc_final: 0.2462 (m-80) REVERT: B 329 PHE cc_start: 0.7299 (m-10) cc_final: 0.6870 (m-80) REVERT: C 740 MET cc_start: 0.5971 (tpt) cc_final: 0.5717 (tpt) REVERT: C 900 MET cc_start: 0.6799 (mtp) cc_final: 0.6232 (mtp) REVERT: C 902 MET cc_start: 0.8136 (mmm) cc_final: 0.7909 (tpt) REVERT: C 904 TYR cc_start: 0.7187 (m-80) cc_final: 0.6980 (m-10) outliers start: 22 outliers final: 9 residues processed: 375 average time/residue: 0.3697 time to fit residues: 217.9462 Evaluate side-chains 192 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 182 time to evaluate : 2.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 739 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 2.9990 chunk 227 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 235 optimal weight: 20.0000 chunk 90 optimal weight: 0.6980 chunk 142 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 chunk 272 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1088 HIS B 343 ASN B 360 ASN B1088 HIS C 314 GLN C1113 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.193370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.163251 restraints weight = 45572.249| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 3.88 r_work: 0.3892 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24423 Z= 0.159 Angle : 0.709 10.794 33295 Z= 0.369 Chirality : 0.048 0.219 3876 Planarity : 0.004 0.043 4251 Dihedral : 7.223 58.199 3847 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.87 % Allowed : 8.03 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.14), residues: 2955 helix: 0.17 (0.19), residues: 645 sheet: -0.53 (0.20), residues: 585 loop : -1.02 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 64 HIS 0.004 0.001 HIS B 207 PHE 0.023 0.002 PHE B 855 TYR 0.021 0.002 TYR B 369 ARG 0.004 0.001 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 30) link_NAG-ASN : angle 3.84040 ( 90) hydrogen bonds : bond 0.05333 ( 1009) hydrogen bonds : angle 6.96047 ( 2718) SS BOND : bond 0.00396 ( 34) SS BOND : angle 1.74939 ( 68) covalent geometry : bond 0.00340 (24359) covalent geometry : angle 0.67774 (33137) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 228 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7997 (mmtt) cc_final: 0.6943 (mtmm) REVERT: A 347 PHE cc_start: 0.2000 (OUTLIER) cc_final: 0.1186 (t80) REVERT: A 697 MET cc_start: 0.7876 (ptm) cc_final: 0.7646 (ptm) REVERT: B 329 PHE cc_start: 0.7771 (m-10) cc_final: 0.7436 (m-80) REVERT: B 357 ARG cc_start: 0.6870 (ttp80) cc_final: 0.6352 (ttp80) REVERT: B 394 ASN cc_start: 0.6548 (m-40) cc_final: 0.5812 (t0) REVERT: B 514 SER cc_start: 0.7714 (m) cc_final: 0.7388 (p) REVERT: C 117 LEU cc_start: 0.8966 (mp) cc_final: 0.8437 (tt) REVERT: C 129 LYS cc_start: 0.8854 (mttm) cc_final: 0.8448 (tmmt) REVERT: C 242 LEU cc_start: 0.7051 (pt) cc_final: 0.6467 (pt) REVERT: C 332 ILE cc_start: 0.7880 (tp) cc_final: 0.7631 (tt) REVERT: C 619 GLU cc_start: 0.5829 (tp30) cc_final: 0.5493 (tp30) REVERT: C 697 MET cc_start: 0.7756 (ptm) cc_final: 0.7502 (ptm) REVERT: C 904 TYR cc_start: 0.7872 (m-80) cc_final: 0.7193 (m-10) outliers start: 49 outliers final: 28 residues processed: 270 average time/residue: 0.3476 time to fit residues: 148.0167 Evaluate side-chains 178 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 140 optimal weight: 40.0000 chunk 168 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 165 optimal weight: 0.6980 chunk 187 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 chunk 166 optimal weight: 0.0070 chunk 280 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 297 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 935 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.193291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.162598 restraints weight = 45350.296| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 3.87 r_work: 0.3928 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 24423 Z= 0.137 Angle : 0.631 12.965 33295 Z= 0.325 Chirality : 0.045 0.171 3876 Planarity : 0.004 0.045 4251 Dihedral : 6.501 58.657 3845 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.07 % Allowed : 9.94 % Favored : 87.99 % 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: -0.77 (0.15), residues: 2955 helix: 0.38 (0.20), residues: 653 sheet: -0.63 (0.20), residues: 615 loop : -0.78 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 64 HIS 0.004 0.001 HIS C1048 PHE 0.018 0.002 PHE B 562 TYR 0.020 0.002 TYR B 789 ARG 0.007 0.001 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 30) link_NAG-ASN : angle 2.95022 ( 90) hydrogen bonds : bond 0.04626 ( 1009) hydrogen bonds : angle 6.44922 ( 2718) SS BOND : bond 0.00267 ( 34) SS BOND : angle 1.60622 ( 68) covalent geometry : bond 0.00292 (24359) covalent geometry : angle 0.60959 (33137) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 191 time to evaluate : 2.442 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 97 LYS cc_start: 0.6261 (pttt) cc_final: 0.5939 (tppt) REVERT: A 298 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6490 (mm-30) REVERT: A 347 PHE cc_start: 0.2600 (OUTLIER) cc_final: 0.1756 (t80) REVERT: A 904 TYR cc_start: 0.5307 (m-10) cc_final: 0.4694 (m-80) REVERT: B 38 TYR cc_start: 0.3875 (m-80) cc_final: 0.2333 (m-80) REVERT: B 242 LEU cc_start: 0.6839 (mm) cc_final: 0.6498 (tp) REVERT: B 514 SER cc_start: 0.7663 (m) cc_final: 0.7423 (p) REVERT: B 577 ARG cc_start: 0.7024 (ttp80) cc_final: 0.6169 (ptm160) REVERT: C 129 LYS cc_start: 0.8767 (mttm) cc_final: 0.8346 (tmmt) REVERT: C 242 LEU cc_start: 0.7277 (pt) cc_final: 0.6890 (pt) REVERT: C 332 ILE cc_start: 0.7991 (tp) cc_final: 0.7768 (tt) REVERT: C 619 GLU cc_start: 0.5837 (tp30) cc_final: 0.5435 (tp30) REVERT: C 902 MET cc_start: 0.8115 (tpp) cc_final: 0.7833 (tpt) REVERT: C 904 TYR cc_start: 0.7793 (m-80) cc_final: 0.7143 (m-10) REVERT: C 973 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7406 (mt) outliers start: 54 outliers final: 32 residues processed: 237 average time/residue: 0.3356 time to fit residues: 127.7629 Evaluate side-chains 184 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 56.9245 > 50: distance: 5 - 22: 6.061 distance: 10 - 33: 5.832 distance: 15 - 41: 7.193 distance: 18 - 22: 3.133 distance: 22 - 23: 4.881 distance: 23 - 24: 6.978 distance: 23 - 26: 7.440 distance: 24 - 25: 8.545 distance: 24 - 33: 7.790 distance: 26 - 27: 8.098 distance: 27 - 28: 11.530 distance: 27 - 29: 9.245 distance: 28 - 30: 6.513 distance: 29 - 31: 15.847 distance: 30 - 32: 5.592 distance: 31 - 32: 11.746 distance: 33 - 34: 5.136 distance: 34 - 35: 5.391 distance: 34 - 37: 5.553 distance: 35 - 36: 8.462 distance: 35 - 41: 4.828 distance: 37 - 38: 9.101 distance: 38 - 39: 11.172 distance: 38 - 40: 18.229 distance: 41 - 42: 14.506 distance: 42 - 43: 7.259 distance: 43 - 44: 4.413 distance: 43 - 45: 4.434 distance: 45 - 46: 5.314 distance: 46 - 47: 5.595 distance: 46 - 49: 6.857 distance: 47 - 48: 10.983 distance: 49 - 50: 12.810 distance: 49 - 51: 14.591 distance: 50 - 52: 9.875 distance: 53 - 54: 10.015 distance: 54 - 55: 12.630 distance: 55 - 56: 3.779 distance: 55 - 57: 14.399 distance: 57 - 58: 16.300 distance: 58 - 59: 29.595 distance: 58 - 61: 13.523 distance: 59 - 60: 8.926 distance: 59 - 64: 10.816 distance: 61 - 62: 8.515 distance: 61 - 63: 9.952 distance: 64 - 65: 9.069 distance: 65 - 66: 4.675 distance: 65 - 68: 3.668 distance: 66 - 67: 10.799 distance: 66 - 71: 9.983 distance: 68 - 69: 8.405 distance: 68 - 70: 14.116 distance: 71 - 72: 8.142 distance: 72 - 73: 5.077 distance: 72 - 75: 14.384 distance: 73 - 74: 7.457 distance: 73 - 80: 11.432 distance: 74 - 103: 9.112 distance: 75 - 76: 18.472 distance: 76 - 77: 8.156 distance: 77 - 78: 21.961 distance: 77 - 79: 17.448 distance: 80 - 81: 11.041 distance: 81 - 82: 13.442 distance: 81 - 84: 8.082 distance: 82 - 83: 5.287 distance: 82 - 88: 5.526 distance: 83 - 113: 22.813 distance: 84 - 85: 15.713 distance: 85 - 86: 5.196 distance: 85 - 87: 17.372 distance: 88 - 89: 22.394 distance: 89 - 90: 20.472 distance: 89 - 92: 24.557 distance: 90 - 95: 34.847 distance: 92 - 93: 14.511 distance: 92 - 94: 25.705