Starting phenix.real_space_refine on Wed Jan 15 20:37:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sgt_10184/01_2025/6sgt_10184_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sgt_10184/01_2025/6sgt_10184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6sgt_10184/01_2025/6sgt_10184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sgt_10184/01_2025/6sgt_10184.map" model { file = "/net/cci-nas-00/data/ceres_data/6sgt_10184/01_2025/6sgt_10184_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sgt_10184/01_2025/6sgt_10184_neut.cif" } resolution = 3.46 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= 0.009 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: 5 Type Number sf(0) Gaussians S 134 5.16 5 C 16626 2.51 5 N 4294 2.21 5 O 4827 1.98 5 H 26299 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.71s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 52180 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 15858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 15858 Classifications: {'peptide': 1034} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 988} Chain: "B" Number of atoms: 15849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 15849 Classifications: {'peptide': 1033} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 987} Chain: "C" Number of atoms: 15850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 15850 Classifications: {'peptide': 1033} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 45, 'TRANS': 987} Chain: "D" Number of atoms: 2336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2336 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 3, 'TRANS': 152} Chain: "E" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2287 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 3, 'TRANS': 148} Time building chain proxies: 18.49, per 1000 atoms: 0.35 Number of scatterers: 52180 At special positions: 0 Unit cell: (151.723, 132.625, 144.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 134 16.00 O 4827 8.00 N 4294 7.00 C 16626 6.00 H 26299 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 10.59 Conformation dependent library (CDL) restraints added in 3.3 seconds 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6224 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 23 sheets defined 55.5% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 Processing helix chain 'A' and resid 8 through 28 removed outlier: 4.075A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU A 28 " --> pdb=" O GLY A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 69 removed outlier: 3.543A pdb=" N ILE A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 112 removed outlier: 3.669A pdb=" N GLN A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 298 through 312 removed outlier: 3.715A pdb=" N THR A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 329 through 334 removed outlier: 3.722A pdb=" N VAL A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 359 removed outlier: 3.679A pdb=" N THR A 343 " --> pdb=" O GLU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 366 removed outlier: 3.635A pdb=" N THR A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 377 through 380 Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 391 through 424 removed outlier: 4.647A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 454 removed outlier: 4.458A pdb=" N ARG A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLY A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 463 through 488 removed outlier: 4.224A pdb=" N TYR A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 486 " --> pdb=" O VAL A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 496 Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.741A pdb=" N GLU A 507 " --> pdb=" O ASP A 504 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 509 " --> pdb=" O GLY A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 538 removed outlier: 4.045A pdb=" N TRP A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 557 removed outlier: 3.893A pdb=" N VAL A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 601 removed outlier: 3.845A pdb=" N THR A 587 " --> pdb=" O THR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 656 removed outlier: 3.631A pdb=" N SER A 656 " --> pdb=" O THR A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 708 removed outlier: 4.430A pdb=" N ALA A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 708 " --> pdb=" O ALA A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 739 Processing helix chain 'A' and resid 744 through 755 Processing helix chain 'A' and resid 784 through 788 Processing helix chain 'A' and resid 837 through 849 Processing helix chain 'A' and resid 860 through 868 removed outlier: 4.849A pdb=" N GLU A 866 " --> pdb=" O MET A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 893 removed outlier: 5.141A pdb=" N ILE A 879 " --> pdb=" O SER A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 903 removed outlier: 4.246A pdb=" N VAL A 901 " --> pdb=" O ILE A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 919 removed outlier: 4.391A pdb=" N GLY A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA A 912 " --> pdb=" O GLY A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 956 removed outlier: 3.783A pdb=" N LEU A 932 " --> pdb=" O GLN A 928 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE A 945 " --> pdb=" O ASN A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 991 removed outlier: 3.503A pdb=" N ALA A 963 " --> pdb=" O GLY A 959 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP A 966 " --> pdb=" O GLU A 962 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 968 " --> pdb=" O THR A 964 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG A 969 " --> pdb=" O LEU A 965 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ARG A 973 " --> pdb=" O ARG A 969 " (cutoff:3.500A) Proline residue: A 974 - end of helix Proline residue: A 988 - end of helix Processing helix chain 'A' and resid 996 through 1009 removed outlier: 3.990A pdb=" N ALA A1002 " --> pdb=" O GLY A 998 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A1007 " --> pdb=" O VAL A1003 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY A1009 " --> pdb=" O THR A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1018 removed outlier: 3.552A pdb=" N THR A1013 " --> pdb=" O GLY A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1033 removed outlier: 4.023A pdb=" N VAL A1024 " --> pdb=" O PHE A1020 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A1033 " --> pdb=" O VAL A1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 28 removed outlier: 3.751A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY B 23 " --> pdb=" O ILE B 19 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 removed outlier: 3.675A pdb=" N VAL B 57 " --> pdb=" O ASP B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 99 through 113 Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 150 through 160 removed outlier: 4.134A pdb=" N ASP B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.953A pdb=" N LYS B 195 " --> pdb=" O ASN B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 210 Processing helix chain 'B' and resid 242 through 247 removed outlier: 3.719A pdb=" N PHE B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 313 removed outlier: 3.535A pdb=" N ALA B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 359 removed outlier: 4.213A pdb=" N ILE B 335 " --> pdb=" O PRO B 331 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL B 341 " --> pdb=" O ILE B 337 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 346 " --> pdb=" O LYS B 342 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET B 355 " --> pdb=" O VAL B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 386 removed outlier: 4.480A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 391 through 400 removed outlier: 3.619A pdb=" N MET B 395 " --> pdb=" O ASN B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 423 removed outlier: 3.746A pdb=" N ASP B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN B 415 " --> pdb=" O VAL B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 454 removed outlier: 3.767A pdb=" N GLY B 436 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLY B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL B 443 " --> pdb=" O GLN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 459 removed outlier: 3.834A pdb=" N PHE B 459 " --> pdb=" O MET B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 488 removed outlier: 4.031A pdb=" N GLN B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 496 Processing helix chain 'B' and resid 511 through 537 removed outlier: 3.671A pdb=" N TRP B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 537 " --> pdb=" O GLY B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 556 Processing helix chain 'B' and resid 583 through 601 removed outlier: 3.745A pdb=" N THR B 587 " --> pdb=" O THR B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 656 removed outlier: 4.265A pdb=" N MET B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 707 Processing helix chain 'B' and resid 733 through 738 removed outlier: 3.758A pdb=" N GLN B 737 " --> pdb=" O GLN B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 755 removed outlier: 3.634A pdb=" N THR B 748 " --> pdb=" O ASN B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 780 Processing helix chain 'B' and resid 785 through 788 Processing helix chain 'B' and resid 801 through 804 No H-bonds generated for 'chain 'B' and resid 801 through 804' Processing helix chain 'B' and resid 836 through 845 removed outlier: 3.826A pdb=" N ALA B 840 " --> pdb=" O SER B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 851 removed outlier: 3.595A pdb=" N LYS B 850 " --> pdb=" O LEU B 847 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 851 " --> pdb=" O ALA B 848 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 847 through 851' Processing helix chain 'B' and resid 861 through 868 removed outlier: 3.936A pdb=" N GLN B 865 " --> pdb=" O GLY B 861 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU B 866 " --> pdb=" O MET B 862 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG B 867 " --> pdb=" O SER B 863 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU B 868 " --> pdb=" O TYR B 864 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 861 through 868' Processing helix chain 'B' and resid 872 through 893 Processing helix chain 'B' and resid 897 through 903 removed outlier: 4.230A pdb=" N VAL B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 919 removed outlier: 3.760A pdb=" N GLY B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA B 912 " --> pdb=" O GLY B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 955 removed outlier: 3.553A pdb=" N LEU B 944 " --> pdb=" O LYS B 940 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE B 945 " --> pdb=" O ASN B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 992 removed outlier: 4.711A pdb=" N ARG B 973 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Proline residue: B 974 - end of helix Proline residue: B 988 - end of helix Processing helix chain 'B' and resid 996 through 1017 removed outlier: 4.045A pdb=" N GLY B1006 " --> pdb=" O ALA B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1033 removed outlier: 3.596A pdb=" N VAL B1022 " --> pdb=" O ALA B1018 " (cutoff:3.500A) Proline residue: B1023 - end of helix Processing helix chain 'C' and resid 8 through 28 removed outlier: 3.673A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA C 26 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE C 27 " --> pdb=" O GLY C 23 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU C 28 " --> pdb=" O GLY C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 99 through 112 removed outlier: 3.731A pdb=" N GLN C 112 " --> pdb=" O GLN C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 150 through 162 removed outlier: 3.596A pdb=" N ASN C 161 " --> pdb=" O TYR C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 189 through 193 Processing helix chain 'C' and resid 199 through 208 removed outlier: 3.757A pdb=" N ALA C 206 " --> pdb=" O ASP C 202 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE C 207 " --> pdb=" O VAL C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 300 through 313 Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 337 through 359 Processing helix chain 'C' and resid 361 through 386 removed outlier: 4.542A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix removed outlier: 3.642A pdb=" N ALA C 371 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Proline residue: C 373 - end of helix removed outlier: 3.610A pdb=" N GLY C 378 " --> pdb=" O VAL C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 406 removed outlier: 4.314A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 423 removed outlier: 4.064A pdb=" N VAL C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA C 421 " --> pdb=" O GLU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 452 removed outlier: 3.799A pdb=" N GLY C 436 " --> pdb=" O ARG C 432 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN C 437 " --> pdb=" O LYS C 433 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 438 " --> pdb=" O SER C 434 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN C 439 " --> pdb=" O MET C 435 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLY C 440 " --> pdb=" O GLY C 436 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ALA C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL C 452 " --> pdb=" O VAL C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 485 removed outlier: 4.022A pdb=" N ALA C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE C 474 " --> pdb=" O PHE C 470 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA C 477 " --> pdb=" O THR C 473 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 493 removed outlier: 4.020A pdb=" N ALA C 491 " --> pdb=" O ILE C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 535 removed outlier: 3.684A pdb=" N TRP C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 558 Processing helix chain 'C' and resid 583 through 601 removed outlier: 3.560A pdb=" N THR C 587 " --> pdb=" O THR C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 642 Processing helix chain 'C' and resid 643 through 655 Processing helix chain 'C' and resid 691 through 708 removed outlier: 3.514A pdb=" N LEU C 695 " --> pdb=" O GLY C 691 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN C 697 " --> pdb=" O GLU C 693 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS C 708 " --> pdb=" O ALA C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 740 Processing helix chain 'C' and resid 742 through 756 removed outlier: 4.093A pdb=" N LEU C 750 " --> pdb=" O ILE C 746 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TRP C 754 " --> pdb=" O LEU C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 787 Processing helix chain 'C' and resid 802 through 804 No H-bonds generated for 'chain 'C' and resid 802 through 804' Processing helix chain 'C' and resid 836 through 850 removed outlier: 3.636A pdb=" N ALA C 848 " --> pdb=" O MET C 844 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS C 850 " --> pdb=" O GLN C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 880 removed outlier: 3.567A pdb=" N GLN C 865 " --> pdb=" O GLY C 861 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG C 867 " --> pdb=" O SER C 863 " (cutoff:3.500A) Proline residue: C 874 - end of helix removed outlier: 3.697A pdb=" N ALA C 878 " --> pdb=" O PRO C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 893 removed outlier: 3.640A pdb=" N CYS C 887 " --> pdb=" O VAL C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 903 removed outlier: 3.832A pdb=" N PHE C 899 " --> pdb=" O TRP C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 919 removed outlier: 3.951A pdb=" N GLY C 908 " --> pdb=" O VAL C 904 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG C 919 " --> pdb=" O ALA C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 955 removed outlier: 4.306A pdb=" N ILE C 945 " --> pdb=" O ASN C 941 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 971 Processing helix chain 'C' and resid 971 through 985 Processing helix chain 'C' and resid 986 through 991 removed outlier: 3.513A pdb=" N VAL C 990 " --> pdb=" O VAL C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1017 removed outlier: 4.485A pdb=" N GLY C1006 " --> pdb=" O ALA C1002 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL C1007 " --> pdb=" O VAL C1003 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL C1016 " --> pdb=" O VAL C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1033 Proline residue: C1023 - end of helix Processing helix chain 'D' and resid 14 through 25 removed outlier: 3.580A pdb=" N LEU D 18 " --> pdb=" O LEU D 14 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 36 Processing helix chain 'D' and resid 49 through 58 Processing helix chain 'D' and resid 62 through 67 removed outlier: 4.088A pdb=" N LEU D 67 " --> pdb=" O VAL D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 91 removed outlier: 3.580A pdb=" N LEU D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 100 removed outlier: 4.232A pdb=" N VAL D 98 " --> pdb=" O GLU D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.592A pdb=" N LEU D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 134 Processing helix chain 'D' and resid 148 through 156 removed outlier: 3.583A pdb=" N ILE D 152 " --> pdb=" O THR D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 165 removed outlier: 3.827A pdb=" N LEU D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 22 removed outlier: 3.632A pdb=" N GLU E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 37 Processing helix chain 'E' and resid 49 through 58 Processing helix chain 'E' and resid 59 through 67 removed outlier: 3.921A pdb=" N VAL E 65 " --> pdb=" O GLU E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 91 removed outlier: 4.025A pdb=" N PHE E 90 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 101 removed outlier: 3.566A pdb=" N GLU E 97 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 124 removed outlier: 3.566A pdb=" N LEU E 119 " --> pdb=" O THR E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 134 Processing helix chain 'E' and resid 148 through 157 removed outlier: 3.523A pdb=" N ILE E 152 " --> pdb=" O THR E 148 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER E 153 " --> pdb=" O ALA E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 165 removed outlier: 3.732A pdb=" N LEU E 165 " --> pdb=" O LEU E 161 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 131 removed outlier: 3.601A pdb=" N SER A 80 " --> pdb=" O ARG A 818 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU A 817 " --> pdb=" O SER A 824 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 824 " --> pdb=" O GLU A 817 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.677A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASN A 144 " --> pdb=" O PRO A 285 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A 139 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.677A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 286 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 608 " --> pdb=" O SER A 630 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET A 573 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 182 through 183 Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 268 Processing sheet with id=AA6, first strand: chain 'A' and resid 234 through 235 removed outlier: 5.820A pdb=" N ILE A 235 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE B 731 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 252 through 253 removed outlier: 3.899A pdb=" N LYS A 252 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 717 through 718 removed outlier: 3.666A pdb=" N ASP A 858 " --> pdb=" O GLU A 683 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 805 through 812 removed outlier: 4.165A pdb=" N SER C 233 " --> pdb=" O PRO A 725 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 760 through 764 removed outlier: 4.293A pdb=" N ASN A 760 " --> pdb=" O VAL A 771 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 790 through 792 Processing sheet with id=AB3, first strand: chain 'B' and resid 130 through 131 removed outlier: 3.517A pdb=" N GLU B 130 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL B 43 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR B 93 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER B 80 " --> pdb=" O ARG B 818 " (cutoff:3.500A) removed outlier: 12.335A pdb=" N ARG B 815 " --> pdb=" O GLU B 826 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N GLU B 826 " --> pdb=" O ARG B 815 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU B 817 " --> pdb=" O SER B 824 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASP B 681 " --> pdb=" O THR B 860 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 175 through 178 removed outlier: 4.217A pdb=" N GLY B 288 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASN B 144 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 175 through 178 removed outlier: 4.217A pdb=" N GLY B 288 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA B 286 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER B 608 " --> pdb=" O SER B 630 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 266 through 271 removed outlier: 6.341A pdb=" N MET B 184 " --> pdb=" O TYR B 772 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N MET B 774 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ILE B 186 " --> pdb=" O MET B 774 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN B 760 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL B 773 " --> pdb=" O TYR B 758 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N TYR B 758 " --> pdb=" O VAL B 773 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 217 through 219 removed outlier: 4.201A pdb=" N GLY B 217 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 232 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N SER B 233 " --> pdb=" O PHE C 727 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE C 729 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE B 235 " --> pdb=" O ILE C 729 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 790 through 792 Processing sheet with id=AB9, first strand: chain 'C' and resid 128 through 130 removed outlier: 3.617A pdb=" N SER C 80 " --> pdb=" O ARG C 818 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU C 817 " --> pdb=" O SER C 824 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP C 681 " --> pdb=" O THR C 860 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 175 through 177 removed outlier: 6.798A pdb=" N VAL C 139 " --> pdb=" O PRO C 326 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 267 through 269 removed outlier: 6.124A pdb=" N MET C 184 " --> pdb=" O TYR C 772 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N MET C 774 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ILE C 186 " --> pdb=" O MET C 774 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN C 760 " --> pdb=" O VAL C 771 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL C 773 " --> pdb=" O TYR C 758 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N TYR C 758 " --> pdb=" O VAL C 773 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 252 through 253 removed outlier: 3.688A pdb=" N LYS C 252 " --> pdb=" O VAL C 260 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 284 through 285 removed outlier: 4.388A pdb=" N SER C 608 " --> pdb=" O SER C 630 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET C 573 " --> pdb=" O PHE C 666 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 790 through 792 1397 hydrogen bonds defined for protein. 4005 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: 17.92 Time building geometry restraints manager: 12.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 26293 1.03 - 1.22: 15 1.22 - 1.42: 10636 1.42 - 1.61: 15462 1.61 - 1.81: 262 Bond restraints: 52668 Sorted by residual: bond pdb=" C ASP B 407 " pdb=" O ASP B 407 " ideal model delta sigma weight residual 1.237 1.162 0.074 1.19e-02 7.06e+03 3.91e+01 bond pdb=" C ASP B 164 " pdb=" O ASP B 164 " ideal model delta sigma weight residual 1.237 1.165 0.072 1.16e-02 7.43e+03 3.86e+01 bond pdb=" C MET B 355 " pdb=" O MET B 355 " ideal model delta sigma weight residual 1.236 1.166 0.070 1.29e-02 6.01e+03 2.92e+01 bond pdb=" C TYR A 545 " pdb=" O TYR A 545 " ideal model delta sigma weight residual 1.237 1.192 0.044 1.17e-02 7.31e+03 1.43e+01 bond pdb=" C ALA B 26 " pdb=" O ALA B 26 " ideal model delta sigma weight residual 1.235 1.188 0.046 1.25e-02 6.40e+03 1.37e+01 ... (remaining 52663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 91719 1.40 - 2.79: 3425 2.79 - 4.19: 312 4.19 - 5.58: 63 5.58 - 6.98: 12 Bond angle restraints: 95531 Sorted by residual: angle pdb=" CA TYR A 545 " pdb=" C TYR A 545 " pdb=" O TYR A 545 " ideal model delta sigma weight residual 120.55 114.27 6.28 1.06e+00 8.90e-01 3.51e+01 angle pdb=" N ILE D 62 " pdb=" CA ILE D 62 " pdb=" C ILE D 62 " ideal model delta sigma weight residual 111.62 107.42 4.20 7.90e-01 1.60e+00 2.82e+01 angle pdb=" N ILE C 827 " pdb=" CA ILE C 827 " pdb=" C ILE C 827 " ideal model delta sigma weight residual 113.53 108.43 5.10 9.80e-01 1.04e+00 2.71e+01 angle pdb=" C ASP B 164 " pdb=" N ALA B 165 " pdb=" CA ALA B 165 " ideal model delta sigma weight residual 120.44 126.42 -5.98 1.30e+00 5.92e-01 2.12e+01 angle pdb=" CA TYR B 811 " pdb=" C TYR B 811 " pdb=" O TYR B 811 " ideal model delta sigma weight residual 121.58 116.75 4.83 1.12e+00 7.97e-01 1.86e+01 ... (remaining 95526 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 22027 17.39 - 34.77: 2035 34.77 - 52.16: 496 52.16 - 69.55: 132 69.55 - 86.94: 10 Dihedral angle restraints: 24700 sinusoidal: 13507 harmonic: 11193 Sorted by residual: dihedral pdb=" CA PHE A 388 " pdb=" C PHE A 388 " pdb=" N SER A 389 " pdb=" CA SER A 389 " ideal model delta harmonic sigma weight residual 180.00 -151.97 -28.03 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA ALA A 832 " pdb=" C ALA A 832 " pdb=" N PRO A 833 " pdb=" CA PRO A 833 " ideal model delta harmonic sigma weight residual 180.00 152.76 27.24 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA PHE B 804 " pdb=" C PHE B 804 " pdb=" N SER B 805 " pdb=" CA SER B 805 " ideal model delta harmonic sigma weight residual -180.00 -154.23 -25.77 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 24697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3336 0.045 - 0.091: 669 0.091 - 0.136: 195 0.136 - 0.181: 10 0.181 - 0.227: 2 Chirality restraints: 4212 Sorted by residual: chirality pdb=" CA TYR B 811 " pdb=" N TYR B 811 " pdb=" C TYR B 811 " pdb=" CB TYR B 811 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE B1019 " pdb=" CA ILE B1019 " pdb=" CG1 ILE B1019 " pdb=" CG2 ILE B1019 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA LEU A 219 " pdb=" N LEU A 219 " pdb=" C LEU A 219 " pdb=" CB LEU A 219 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.42e-01 ... (remaining 4209 not shown) Planarity restraints: 7858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 27 " -0.033 2.00e-02 2.50e+03 6.48e-02 4.20e+01 pdb=" N ASP E 28 " 0.111 2.00e-02 2.50e+03 pdb=" CA ASP E 28 " -0.028 2.00e-02 2.50e+03 pdb=" H ASP E 28 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 535 " 0.023 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" N ARG A 536 " -0.076 2.00e-02 2.50e+03 pdb=" CA ARG A 536 " 0.020 2.00e-02 2.50e+03 pdb=" H ARG A 536 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 164 " 0.022 2.00e-02 2.50e+03 4.18e-02 1.74e+01 pdb=" N ALA C 165 " -0.072 2.00e-02 2.50e+03 pdb=" CA ALA C 165 " 0.019 2.00e-02 2.50e+03 pdb=" H ALA C 165 " 0.031 2.00e-02 2.50e+03 ... (remaining 7855 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 2064 2.16 - 2.77: 103970 2.77 - 3.38: 145639 3.38 - 3.99: 189719 3.99 - 4.60: 301607 Nonbonded interactions: 742999 Sorted by model distance: nonbonded pdb=" OE1 GLU E 127 " pdb=" H GLU E 127 " model vdw 1.549 2.450 nonbonded pdb=" OE1 GLU E 94 " pdb=" H GLU E 94 " model vdw 1.602 2.450 nonbonded pdb="HE21 GLN B 181 " pdb=" OE2 GLU B 273 " model vdw 1.604 2.450 nonbonded pdb=" O GLY A 766 " pdb="HE22 GLN B 63 " model vdw 1.612 2.450 nonbonded pdb=" O ILE A 235 " pdb=" H ILE B 729 " model vdw 1.615 2.450 ... (remaining 742994 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 1 through 144 or (resid 145 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 146 through 1033)) selection = (chain 'B' and (resid 1 through 355 or (resid 356 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ or name OH or name H or name HA or name HB2 or name HB3 or name HD \ 1 or name HD2 or name HE1 or name HE2)) or resid 357 through 666 or (resid 667 a \ nd (name N or name CA or name C or name O or name CB or name CG or name OD1 or n \ ame ND2 or name H or name HA or name HB2 or name HB3)) or resid 668 through 1033 \ )) selection = (chain 'C' and (resid 1 through 144 or (resid 145 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 146 through 355 or (resid 356 \ and (name N or name CA or name C or name O or name CB or name CG or name CD1 or \ name CD2 or name CE1 or name CE2 or name CZ or name OH or name H or name HA or n \ ame HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2)) or resid 3 \ 57 through 666 or (resid 667 and (name N or name CA or name C or name O or name \ CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name H \ B3)) or resid 668 through 1033)) } ncs_group { reference = (chain 'D' and ((resid 15 and (name N or name CA or name C or name O or name HA2 \ or name HA3)) or resid 16 through 166)) selection = chain 'E' } 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: 1.600 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: 0.680 Extract box with map and model: 1.450 Check model and map are aligned: 0.290 Set scattering table: 0.370 Process input model: 82.950 Find NCS groups from input model: 1.480 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 26369 Z= 0.281 Angle : 0.721 6.702 35814 Z= 0.447 Chirality : 0.040 0.227 4212 Planarity : 0.004 0.041 4596 Dihedral : 12.561 86.936 9508 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.53 % Favored : 95.38 % Rotamer: Outliers : 0.29 % Allowed : 2.72 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: -4.71 (0.11), residues: 3398 helix: -2.87 (0.09), residues: 1761 sheet: -2.73 (0.21), residues: 411 loop : -3.38 (0.14), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 809 HIS 0.003 0.001 HIS E 89 PHE 0.015 0.001 PHE C 11 TYR 0.037 0.002 TYR B 356 ARG 0.012 0.001 ARG A 818 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 796 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 788 time to evaluate : 2.979 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: 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: 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: 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: 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: symmetry clash REVERT: A 59 ASP cc_start: 0.7531 (m-30) cc_final: 0.7293 (m-30) REVERT: A 134 SER cc_start: 0.8181 (m) cc_final: 0.7891 (t) REVERT: A 512 PHE cc_start: 0.6740 (t80) cc_final: 0.6156 (t80) REVERT: A 1030 ARG cc_start: 0.7883 (mmm-85) cc_final: 0.7488 (ttm-80) REVERT: B 38 ILE cc_start: 0.8175 (pt) cc_final: 0.7952 (pt) REVERT: B 686 ASP cc_start: 0.8045 (p0) cc_final: 0.7526 (p0) REVERT: B 841 MET cc_start: 0.8340 (mtt) cc_final: 0.8066 (mtm) REVERT: B 992 SER cc_start: 0.7946 (t) cc_final: 0.7732 (m) REVERT: C 388 PHE cc_start: 0.6691 (m-10) cc_final: 0.6315 (m-80) REVERT: C 746 ILE cc_start: 0.8418 (pt) cc_final: 0.8185 (pt) REVERT: C 1032 ARG cc_start: 0.6857 (tpp80) cc_final: 0.6510 (mmt180) outliers start: 8 outliers final: 1 residues processed: 794 average time/residue: 0.8160 time to fit residues: 978.3290 Evaluate side-chains 484 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 483 time to evaluate : 2.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 286 optimal weight: 7.9990 chunk 256 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 265 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 307 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 ASN A 642 ASN A 667 ASN A 846 GLN A1000 GLN B 89 GLN B 284 GLN B 697 GLN B 700 ASN C 161 ASN C 231 ASN C 255 GLN C 298 ASN C 360 GLN C 415 ASN C 526 HIS C 605 ASN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1000 GLN C1001 ASN D 102 ASN D 156 ASN E 74 ASN E 102 ASN E 166 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.142807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.127427 restraints weight = 99915.491| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.38 r_work: 0.3293 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 26369 Z= 0.352 Angle : 0.678 10.491 35814 Z= 0.363 Chirality : 0.044 0.181 4212 Planarity : 0.004 0.049 4596 Dihedral : 5.417 44.113 3611 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.74 % Allowed : 10.20 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: -2.94 (0.13), residues: 3398 helix: -1.23 (0.12), residues: 1769 sheet: -2.25 (0.22), residues: 429 loop : -2.75 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 13 HIS 0.007 0.001 HIS C 709 PHE 0.033 0.002 PHE B 615 TYR 0.017 0.002 TYR A 758 ARG 0.007 0.001 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 549 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 501 time to evaluate : 2.983 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: 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: 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 134 SER cc_start: 0.8606 (m) cc_final: 0.8382 (t) REVERT: A 274 ASN cc_start: 0.8071 (OUTLIER) cc_final: 0.7807 (p0) REVERT: A 445 ILE cc_start: 0.8593 (mm) cc_final: 0.8376 (mt) REVERT: A 458 PHE cc_start: 0.7089 (m-10) cc_final: 0.6802 (m-10) REVERT: A 554 TYR cc_start: 0.8285 (t80) cc_final: 0.8075 (t80) REVERT: A 681 ASP cc_start: 0.7754 (t0) cc_final: 0.7540 (t0) REVERT: A 980 LEU cc_start: 0.8490 (tt) cc_final: 0.8155 (mp) REVERT: A 1011 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7761 (mmt) REVERT: B 156 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.8324 (t0) REVERT: B 164 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.7921 (m-30) REVERT: B 355 MET cc_start: 0.7768 (mtp) cc_final: 0.7351 (mtp) REVERT: B 359 LEU cc_start: 0.8138 (mm) cc_final: 0.7871 (mt) REVERT: B 556 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.6277 (m-80) REVERT: B 686 ASP cc_start: 0.8349 (p0) cc_final: 0.8116 (p0) REVERT: B 978 THR cc_start: 0.8231 (m) cc_final: 0.7894 (p) REVERT: C 156 ASP cc_start: 0.8363 (t0) cc_final: 0.8113 (t0) REVERT: C 746 ILE cc_start: 0.8824 (pt) cc_final: 0.8616 (pt) REVERT: C 1032 ARG cc_start: 0.7226 (tpp80) cc_final: 0.6787 (mmt180) REVERT: D 41 ASN cc_start: 0.6698 (m-40) cc_final: 0.6411 (m-40) REVERT: E 102 ASN cc_start: 0.7446 (OUTLIER) cc_final: 0.7123 (t0) REVERT: E 110 ASP cc_start: 0.8361 (m-30) cc_final: 0.8034 (m-30) REVERT: E 134 LYS cc_start: 0.7360 (ttmm) cc_final: 0.7124 (ptmt) outliers start: 48 outliers final: 31 residues processed: 536 average time/residue: 0.7507 time to fit residues: 644.3997 Evaluate side-chains 461 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 424 time to evaluate : 2.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 525 HIS Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 795 ASP Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 757 SER Chi-restraints excluded: chain C residue 810 GLU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain E residue 102 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 213 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 chunk 275 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 ASN A 928 GLN B 284 GLN C 63 GLN C 526 HIS C 657 GLN C 747 ASN C1000 GLN C1001 ASN ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.133193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.117473 restraints weight = 103651.762| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.35 r_work: 0.3266 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 26369 Z= 0.316 Angle : 0.620 8.365 35814 Z= 0.330 Chirality : 0.043 0.159 4212 Planarity : 0.004 0.049 4596 Dihedral : 5.253 46.040 3611 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.63 % Allowed : 12.23 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: -2.31 (0.14), residues: 3398 helix: -0.71 (0.12), residues: 1796 sheet: -2.08 (0.22), residues: 425 loop : -2.45 (0.16), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 789 HIS 0.011 0.001 HIS E 89 PHE 0.021 0.001 PHE B 615 TYR 0.014 0.002 TYR A 541 ARG 0.004 0.000 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 498 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 453 time to evaluate : 2.993 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: 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 134 SER cc_start: 0.8567 (m) cc_final: 0.8366 (t) REVERT: A 274 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7873 (p0) REVERT: A 448 VAL cc_start: 0.8139 (m) cc_final: 0.7926 (t) REVERT: A 458 PHE cc_start: 0.7221 (m-10) cc_final: 0.6954 (m-10) REVERT: A 512 PHE cc_start: 0.7061 (t80) cc_final: 0.6788 (t80) REVERT: B 87 THR cc_start: 0.8864 (t) cc_final: 0.8625 (m) REVERT: B 556 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.6255 (m-80) REVERT: B 686 ASP cc_start: 0.8363 (p0) cc_final: 0.8150 (p0) REVERT: B 882 ILE cc_start: 0.9204 (mt) cc_final: 0.8980 (mt) REVERT: C 366 LEU cc_start: 0.8673 (mt) cc_final: 0.8416 (tp) REVERT: C 746 ILE cc_start: 0.8801 (pt) cc_final: 0.8514 (pt) REVERT: C 1032 ARG cc_start: 0.7220 (tpp80) cc_final: 0.6814 (mmt180) REVERT: D 41 ASN cc_start: 0.6670 (m-40) cc_final: 0.6363 (m-40) REVERT: E 110 ASP cc_start: 0.8406 (m-30) cc_final: 0.8078 (m-30) REVERT: E 134 LYS cc_start: 0.7422 (ttmm) cc_final: 0.7192 (ptmt) outliers start: 45 outliers final: 33 residues processed: 483 average time/residue: 0.6809 time to fit residues: 530.9834 Evaluate side-chains 451 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 416 time to evaluate : 2.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 666 PHE Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 525 HIS Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 795 ASP Chi-restraints excluded: chain B residue 804 PHE Chi-restraints excluded: chain B residue 844 MET Chi-restraints excluded: chain B residue 910 ILE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 810 GLU Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 147 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 315 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 258 optimal weight: 1.9990 chunk 309 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 283 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN A 605 ASN B 719 ASN C 63 GLN C 67 GLN C 213 GLN C 237 GLN C 605 ASN E 102 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.136983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.121404 restraints weight = 102181.579| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.39 r_work: 0.3215 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 26369 Z= 0.333 Angle : 0.621 8.486 35814 Z= 0.330 Chirality : 0.043 0.160 4212 Planarity : 0.004 0.055 4596 Dihedral : 5.112 26.771 3609 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.25 % Allowed : 12.99 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: -1.92 (0.14), residues: 3398 helix: -0.39 (0.12), residues: 1798 sheet: -2.05 (0.22), residues: 444 loop : -2.20 (0.17), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 48 HIS 0.006 0.001 HIS C 709 PHE 0.030 0.002 PHE B 615 TYR 0.016 0.002 TYR A 758 ARG 0.010 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 493 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 431 time to evaluate : 2.967 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: 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 4 PHE cc_start: 0.4905 (t80) cc_final: 0.4637 (m-80) REVERT: A 274 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.8029 (p0) REVERT: A 458 PHE cc_start: 0.7497 (m-10) cc_final: 0.7272 (m-10) REVERT: A 512 PHE cc_start: 0.7154 (t80) cc_final: 0.6919 (t80) REVERT: B 87 THR cc_start: 0.8877 (t) cc_final: 0.8645 (m) REVERT: B 556 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.6282 (m-80) REVERT: B 686 ASP cc_start: 0.8498 (p0) cc_final: 0.8263 (p0) REVERT: B 767 ARG cc_start: 0.7868 (tpp80) cc_final: 0.7589 (tpp80) REVERT: C 313 MET cc_start: 0.8702 (ptp) cc_final: 0.8475 (ptp) REVERT: C 366 LEU cc_start: 0.8732 (mt) cc_final: 0.8457 (tp) REVERT: C 558 ARG cc_start: 0.7694 (ptp-170) cc_final: 0.6896 (ptt90) REVERT: C 603 LYS cc_start: 0.8657 (ptmt) cc_final: 0.8149 (pttm) REVERT: C 746 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8645 (pt) REVERT: C 951 ASP cc_start: 0.5997 (OUTLIER) cc_final: 0.5472 (m-30) REVERT: C 1032 ARG cc_start: 0.7390 (tpp80) cc_final: 0.6923 (mmt180) REVERT: D 41 ASN cc_start: 0.6646 (m-40) cc_final: 0.6307 (m-40) REVERT: D 127 GLU cc_start: 0.6864 (pm20) cc_final: 0.6462 (pt0) REVERT: E 110 ASP cc_start: 0.8423 (m-30) cc_final: 0.8103 (m-30) outliers start: 62 outliers final: 45 residues processed: 471 average time/residue: 0.6959 time to fit residues: 524.5469 Evaluate side-chains 453 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 404 time to evaluate : 2.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 666 PHE Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 525 HIS Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 569 GLN Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 795 ASP Chi-restraints excluded: chain B residue 804 PHE Chi-restraints excluded: chain B residue 844 MET Chi-restraints excluded: chain B residue 910 ILE Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 757 SER Chi-restraints excluded: chain C residue 810 GLU Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 951 ASP Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 200 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 192 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 334 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 309 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 0.0980 chunk 206 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 605 ASN A 726 GLN B 144 ASN C 213 GLN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.129511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.113131 restraints weight = 104870.810| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.45 r_work: 0.3190 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 26369 Z= 0.315 Angle : 0.611 8.242 35814 Z= 0.323 Chirality : 0.043 0.162 4212 Planarity : 0.004 0.052 4596 Dihedral : 5.033 27.600 3609 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.47 % Allowed : 14.05 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: -1.58 (0.14), residues: 3398 helix: -0.13 (0.12), residues: 1804 sheet: -1.97 (0.23), residues: 425 loop : -2.01 (0.17), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 48 HIS 0.006 0.001 HIS C 709 PHE 0.031 0.002 PHE B 615 TYR 0.016 0.002 TYR A 758 ARG 0.003 0.000 ARG A 818 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 504 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 436 time to evaluate : 3.532 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: 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 355 MET cc_start: 0.8134 (mmm) cc_final: 0.7319 (mmm) REVERT: A 641 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7538 (pm20) REVERT: A 892 TYR cc_start: 0.8473 (m-80) cc_final: 0.8092 (m-80) REVERT: A 894 SER cc_start: 0.8869 (t) cc_final: 0.8626 (m) REVERT: A 1030 ARG cc_start: 0.8597 (mmm-85) cc_final: 0.8023 (ttm-80) REVERT: B 87 THR cc_start: 0.8908 (t) cc_final: 0.8685 (m) REVERT: B 202 ASP cc_start: 0.7343 (p0) cc_final: 0.6357 (t0) REVERT: B 556 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.6254 (m-80) REVERT: B 686 ASP cc_start: 0.8535 (p0) cc_final: 0.8332 (p0) REVERT: C 313 MET cc_start: 0.8736 (ptp) cc_final: 0.8484 (ptp) REVERT: C 366 LEU cc_start: 0.8729 (mt) cc_final: 0.8427 (tp) REVERT: C 558 ARG cc_start: 0.7722 (ptp-170) cc_final: 0.6850 (ptt90) REVERT: C 603 LYS cc_start: 0.8722 (ptmt) cc_final: 0.8190 (pttm) REVERT: C 746 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8617 (pt) REVERT: C 951 ASP cc_start: 0.6044 (OUTLIER) cc_final: 0.5446 (m-30) REVERT: C 1032 ARG cc_start: 0.7428 (tpp80) cc_final: 0.6988 (mmt180) REVERT: D 41 ASN cc_start: 0.6667 (m-40) cc_final: 0.6295 (m-40) REVERT: D 127 GLU cc_start: 0.6840 (pm20) cc_final: 0.6428 (pt0) REVERT: E 110 ASP cc_start: 0.8440 (m-30) cc_final: 0.8133 (m-30) outliers start: 68 outliers final: 53 residues processed: 479 average time/residue: 0.7347 time to fit residues: 564.3790 Evaluate side-chains 459 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 402 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 666 PHE Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 525 HIS Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 569 GLN Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 795 ASP Chi-restraints excluded: chain B residue 804 PHE Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 910 ILE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 666 PHE Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 757 SER Chi-restraints excluded: chain C residue 810 GLU Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 951 ASP Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 140 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 15 optimal weight: 2.9990 chunk 272 optimal weight: 1.9990 chunk 220 optimal weight: 0.0980 chunk 328 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 276 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 297 optimal weight: 0.8980 chunk 222 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 ASN A 747 ASN C 213 GLN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1001 ASN E 166 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.137242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.121627 restraints weight = 102185.289| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.42 r_work: 0.3215 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26369 Z= 0.199 Angle : 0.555 8.471 35814 Z= 0.292 Chirality : 0.040 0.160 4212 Planarity : 0.003 0.058 4596 Dihedral : 4.788 26.424 3609 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.89 % Allowed : 15.25 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: -1.15 (0.14), residues: 3398 helix: 0.21 (0.13), residues: 1807 sheet: -1.78 (0.24), residues: 410 loop : -1.79 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 48 HIS 0.006 0.001 HIS C 709 PHE 0.032 0.001 PHE B 615 TYR 0.013 0.001 TYR A 157 ARG 0.004 0.000 ARG A 792 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 485 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 433 time to evaluate : 3.034 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: 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 274 ASN cc_start: 0.8529 (p0) cc_final: 0.8282 (p0) REVERT: A 355 MET cc_start: 0.8100 (mmm) cc_final: 0.7289 (mmm) REVERT: A 641 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7609 (pm20) REVERT: A 892 TYR cc_start: 0.8493 (m-80) cc_final: 0.8196 (m-80) REVERT: A 894 SER cc_start: 0.8823 (t) cc_final: 0.8614 (m) REVERT: A 980 LEU cc_start: 0.8743 (tt) cc_final: 0.8314 (mp) REVERT: A 1011 MET cc_start: 0.8597 (tpt) cc_final: 0.8397 (tpt) REVERT: A 1030 ARG cc_start: 0.8514 (mmm-85) cc_final: 0.7948 (ttm-80) REVERT: B 87 THR cc_start: 0.8901 (t) cc_final: 0.8691 (m) REVERT: B 202 ASP cc_start: 0.7224 (p0) cc_final: 0.6415 (t0) REVERT: B 353 LEU cc_start: 0.8544 (pp) cc_final: 0.8259 (mt) REVERT: B 556 PHE cc_start: 0.7473 (OUTLIER) cc_final: 0.6322 (m-80) REVERT: C 313 MET cc_start: 0.8711 (ptp) cc_final: 0.8439 (ptp) REVERT: C 366 LEU cc_start: 0.8711 (mt) cc_final: 0.8350 (tt) REVERT: C 558 ARG cc_start: 0.7708 (ptp-170) cc_final: 0.6760 (ptt90) REVERT: C 603 LYS cc_start: 0.8691 (ptmt) cc_final: 0.8241 (pttm) REVERT: C 746 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8446 (pt) REVERT: C 951 ASP cc_start: 0.5989 (OUTLIER) cc_final: 0.5366 (m-30) REVERT: C 1032 ARG cc_start: 0.7401 (tpp80) cc_final: 0.7004 (mmt180) REVERT: D 41 ASN cc_start: 0.6593 (m-40) cc_final: 0.6209 (m-40) REVERT: D 101 LYS cc_start: 0.7902 (mtpp) cc_final: 0.7675 (mtmt) REVERT: D 127 GLU cc_start: 0.6855 (pm20) cc_final: 0.6449 (pt0) REVERT: E 110 ASP cc_start: 0.8418 (m-30) cc_final: 0.8078 (m-30) outliers start: 52 outliers final: 42 residues processed: 466 average time/residue: 0.7222 time to fit residues: 536.6849 Evaluate side-chains 455 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 409 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 666 PHE Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 525 HIS Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 569 GLN Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 795 ASP Chi-restraints excluded: chain B residue 804 PHE Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 910 ILE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 666 PHE Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 757 SER Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 951 ASP Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 138 optimal weight: 3.9990 chunk 210 optimal weight: 0.8980 chunk 265 optimal weight: 3.9990 chunk 328 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 253 optimal weight: 4.9990 chunk 266 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 68 ASN A 74 ASN A 361 ASN A 605 ASN B 588 GLN C 213 GLN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.129002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.112902 restraints weight = 105002.221| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.43 r_work: 0.3180 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 26369 Z= 0.329 Angle : 0.603 8.060 35814 Z= 0.319 Chirality : 0.042 0.168 4212 Planarity : 0.004 0.059 4596 Dihedral : 4.874 27.262 3609 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.14 % Allowed : 15.90 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: -1.16 (0.14), residues: 3398 helix: 0.19 (0.12), residues: 1813 sheet: -1.83 (0.23), residues: 420 loop : -1.75 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 48 HIS 0.005 0.001 HIS C 709 PHE 0.030 0.002 PHE B 615 TYR 0.016 0.002 TYR A 758 ARG 0.003 0.000 ARG A 818 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 356 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Evaluate side-chains 478 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 419 time to evaluate : 3.043 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ASN cc_start: 0.8579 (p0) cc_final: 0.8365 (p0) REVERT: A 355 MET cc_start: 0.8250 (mmm) cc_final: 0.7416 (mmm) REVERT: A 641 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7531 (pm20) REVERT: A 892 TYR cc_start: 0.8610 (m-80) cc_final: 0.8323 (m-80) REVERT: A 894 SER cc_start: 0.8860 (t) cc_final: 0.8629 (m) REVERT: B 202 ASP cc_start: 0.7485 (p0) cc_final: 0.6592 (t0) REVERT: B 353 LEU cc_start: 0.8633 (pp) cc_final: 0.8278 (mt) REVERT: B 556 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.6464 (m-80) REVERT: C 313 MET cc_start: 0.8730 (ptp) cc_final: 0.8489 (ptp) REVERT: C 366 LEU cc_start: 0.8807 (mt) cc_final: 0.8414 (tt) REVERT: C 541 TYR cc_start: 0.7535 (m-80) cc_final: 0.7234 (m-80) REVERT: C 558 ARG cc_start: 0.7742 (ptp-170) cc_final: 0.6792 (ptt90) REVERT: C 603 LYS cc_start: 0.8765 (ptmt) cc_final: 0.8284 (pttm) REVERT: C 951 ASP cc_start: 0.6098 (OUTLIER) cc_final: 0.5426 (m-30) REVERT: D 41 ASN cc_start: 0.6663 (m-40) cc_final: 0.6267 (m-40) REVERT: D 101 LYS cc_start: 0.7756 (mtpp) cc_final: 0.7501 (mtmt) REVERT: E 110 ASP cc_start: 0.8398 (m-30) cc_final: 0.8106 (m-30) outliers start: 59 outliers final: 49 residues processed: 459 average time/residue: 0.7436 time to fit residues: 545.5354 Evaluate side-chains 459 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 407 time to evaluate : 3.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 666 PHE Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 525 HIS Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 569 GLN Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 795 ASP Chi-restraints excluded: chain B residue 804 PHE Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 666 PHE Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 757 SER Chi-restraints excluded: chain C residue 810 GLU Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 951 ASP Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 50.2366 > 50: distance: 7 - 23: 3.125 distance: 26 - 50: 3.161 distance: 191 - 231: 5.087 distance: 206 - 250: 6.223 distance: 213 - 260: 6.372 distance: 222 - 231: 6.140 distance: 223 - 280: 8.197 distance: 231 - 232: 4.461 distance: 231 - 239: 20.524 distance: 232 - 233: 11.324 distance: 232 - 235: 9.442 distance: 232 - 240: 4.756 distance: 233 - 234: 7.578 distance: 233 - 250: 10.946 distance: 234 - 299: 16.754 distance: 235 - 236: 5.704 distance: 235 - 241: 14.283 distance: 235 - 242: 9.790 distance: 236 - 237: 7.390 distance: 236 - 238: 4.038 distance: 236 - 243: 4.319 distance: 237 - 244: 9.477 distance: 237 - 245: 3.225 distance: 237 - 246: 8.460 distance: 238 - 247: 6.925 distance: 238 - 248: 5.120 distance: 250 - 251: 10.824 distance: 250 - 255: 18.132 distance: 251 - 252: 14.424 distance: 251 - 254: 3.635 distance: 251 - 256: 8.969 distance: 252 - 253: 19.388 distance: 252 - 260: 12.801 distance: 253 - 318: 21.318 distance: 254 - 257: 10.490 distance: 254 - 258: 3.934 distance: 254 - 259: 9.321 distance: 260 - 261: 7.053 distance: 260 - 271: 17.139 distance: 261 - 262: 12.785 distance: 261 - 264: 11.806 distance: 261 - 272: 11.361 distance: 262 - 263: 13.070 distance: 262 - 280: 11.772 distance: 264 - 265: 3.831 distance: 264 - 273: 6.210 distance: 264 - 274: 4.359 distance: 266 - 268: 3.213 distance: 266 - 275: 3.392 distance: 268 - 277: 3.615 distance: 269 - 278: 4.397 distance: 280 - 281: 13.045 distance: 280 - 288: 6.795 distance: 281 - 282: 16.153 distance: 281 - 284: 6.744 distance: 281 - 289: 7.197 distance: 282 - 283: 18.130 distance: 282 - 299: 13.799 distance: 284 - 285: 5.070 distance: 284 - 286: 8.111 distance: 284 - 290: 9.065 distance: 285 - 287: 7.760 distance: 285 - 291: 3.680 distance: 285 - 292: 4.510 distance: 286 - 293: 14.959 distance: 286 - 294: 14.957 distance: 286 - 295: 14.833 distance: 287 - 297: 3.335 distance: 299 - 300: 27.420 distance: 299 - 307: 10.851 distance: 300 - 301: 16.960 distance: 300 - 303: 6.060 distance: 300 - 308: 14.802 distance: 301 - 302: 14.711 distance: 301 - 318: 14.335 distance: 303 - 304: 14.565 distance: 303 - 309: 13.271 distance: 303 - 310: 9.349 distance: 304 - 305: 14.955 distance: 304 - 306: 5.602 distance: 304 - 311: 5.479 distance: 305 - 312: 10.743 distance: 305 - 313: 8.354 distance: 305 - 314: 11.628 distance: 306 - 315: 10.159 distance: 318 - 319: 10.620 distance: 318 - 322: 16.604 distance: 319 - 320: 12.291 distance: 319 - 323: 27.678 distance: 319 - 324: 18.708 distance: 320 - 321: 20.081 distance: 320 - 325: 6.407 distance: 325 - 326: 5.876 distance: 325 - 332: 6.322 distance: 326 - 327: 18.009 distance: 326 - 329: 9.125 distance: 326 - 333: 20.137 distance: 327 - 328: 9.257 distance: 327 - 341: 12.804 distance: 329 - 330: 13.292 distance: 329 - 331: 16.357 distance: 329 - 334: 17.550 distance: 330 - 335: 20.580 distance: 330 - 336: 11.834 distance: 330 - 337: 18.504 distance: 331 - 338: 8.658 distance: 331 - 339: 10.722 distance: 331 - 340: 13.175 distance: 341 - 342: 4.825 distance: 341 - 349: 19.674 distance: 342 - 343: 18.079 distance: 342 - 345: 12.017 distance: 342 - 350: 19.887 distance: 343 - 344: 17.827 distance: 343 - 358: 12.061 distance: 344 - 406: 24.901 distance: 345 - 346: 13.012 distance: 345 - 351: 21.459 distance: 345 - 352: 20.440 distance: 346 - 347: 18.270 distance: 346 - 353: 14.259 distance: 346 - 354: 5.390 distance: 347 - 348: 20.686 distance: 348 - 355: 4.360 distance: 348 - 356: 7.401 distance: 358 - 359: 10.536 distance: 358 - 364: 4.381 distance: 359 - 360: 9.627 distance: 359 - 362: 6.860 distance: 359 - 365: 13.621 distance: 360 - 361: 13.883 distance: 360 - 372: 15.534 distance: 362 - 363: 9.389 distance: 362 - 367: 5.053 distance: 363 - 364: 10.753 distance: 363 - 368: 15.108 distance: 363 - 369: 22.627 distance: 364 - 370: 15.798 distance: 364 - 371: 13.898 distance: 372 - 373: 8.372 distance: 372 - 380: 11.702 distance: 373 - 376: 4.710 distance: 373 - 381: 4.237 distance: 374 - 375: 6.123 distance: 376 - 377: 7.827 distance: 376 - 382: 8.096 distance: 376 - 383: 10.214 distance: 377 - 378: 10.895 distance: 377 - 379: 7.301 distance: 377 - 384: 9.108 distance: 378 - 385: 10.985 distance: 378 - 386: 7.180 distance: 378 - 387: 7.844 distance: 379 - 388: 8.313 distance: 379 - 389: 7.502 distance: 379 - 390: 17.237