Starting phenix.real_space_refine on Fri Jun 20 19:57:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7swl_25474/06_2025/7swl_25474.cif Found real_map, /net/cci-nas-00/data/ceres_data/7swl_25474/06_2025/7swl_25474.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7swl_25474/06_2025/7swl_25474.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7swl_25474/06_2025/7swl_25474.map" model { file = "/net/cci-nas-00/data/ceres_data/7swl_25474/06_2025/7swl_25474.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7swl_25474/06_2025/7swl_25474.cif" } resolution = 2.88 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 ------------------------------------------------------------------------------- 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= 0.049 sd= 0.336 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: 6 Type Number sf(0) Gaussians P 29 5.49 5 Mg 9 5.21 5 S 115 5.16 5 C 14929 2.51 5 N 4252 2.21 5 O 4573 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23907 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4238 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 523} Chain breaks: 4 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 4262 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 551, 4246 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 522} Chain breaks: 4 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 551, 4246 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 522} Chain breaks: 4 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4294 Chain: "C" Number of atoms: 4320 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 559, 4306 Classifications: {'peptide': 559} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 530} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 559, 4306 Classifications: {'peptide': 559} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 530} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 4357 Chain: "D" Number of atoms: 4259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4259 Classifications: {'peptide': 555} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 525} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 3652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3652 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 456} Chain breaks: 6 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2684 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 329} Chain breaks: 7 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 177 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 19.58, per 1000 atoms: 0.82 Number of scatterers: 23907 At special positions: 0 Unit cell: (127.595, 146.575, 158.175, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 115 16.00 P 29 15.00 Mg 9 11.99 O 4573 8.00 N 4252 7.00 C 14929 6.00 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: 6.55 Conformation dependent library (CDL) restraints added in 4.5 seconds 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5698 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 11 sheets defined 61.7% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 207 through 218 removed outlier: 3.844A pdb=" N LYS A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 224 through 232 removed outlier: 3.983A pdb=" N CYS A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 removed outlier: 3.585A pdb=" N GLY A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 removed outlier: 4.297A pdb=" N ILE A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 269 through 273' Processing helix chain 'A' and resid 276 through 294 removed outlier: 4.274A pdb=" N GLU A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 287 " --> pdb=" O ASN A 283 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 307 Processing helix chain 'A' and resid 318 through 336 removed outlier: 3.965A pdb=" N VAL A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP A 331 " --> pdb=" O MET A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 407 through 423 Processing helix chain 'A' and resid 423 through 438 removed outlier: 3.682A pdb=" N LEU A 430 " --> pdb=" O ASN A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 460 removed outlier: 3.977A pdb=" N HIS A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 483 removed outlier: 3.711A pdb=" N PHE A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 481 " --> pdb=" O ARG A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 506 through 517 Processing helix chain 'A' and resid 517 through 523 Processing helix chain 'A' and resid 523 through 529 Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 577 through 593 removed outlier: 3.646A pdb=" N VAL A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 606 Processing helix chain 'A' and resid 614 through 632 removed outlier: 4.380A pdb=" N SER A 618 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA A 619 " --> pdb=" O SER A 615 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ARG A 620 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 650 removed outlier: 3.647A pdb=" N ILE A 650 " --> pdb=" O PRO A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 656 removed outlier: 3.772A pdb=" N ARG A 656 " --> pdb=" O ALA A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 686 removed outlier: 3.658A pdb=" N VAL A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 725 removed outlier: 3.586A pdb=" N GLU A 720 " --> pdb=" O ASP A 716 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 721 " --> pdb=" O ALA A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 729 Processing helix chain 'A' and resid 732 through 755 Processing helix chain 'A' and resid 755 through 760 Processing helix chain 'A' and resid 776 through 786 removed outlier: 3.578A pdb=" N LYS A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN A 785 " --> pdb=" O GLU A 781 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A 786 " --> pdb=" O LYS A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 799 removed outlier: 4.323A pdb=" N TYR A 797 " --> pdb=" O ASP A 793 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET A 798 " --> pdb=" O PRO A 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 207 through 218 removed outlier: 4.201A pdb=" N LYS B 216 " --> pdb=" O GLN B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 224 removed outlier: 3.531A pdb=" N LEU B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 231 removed outlier: 3.578A pdb=" N CYS B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 270 through 273 Processing helix chain 'B' and resid 278 through 294 removed outlier: 3.658A pdb=" N ILE B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 307 Processing helix chain 'B' and resid 316 through 337 removed outlier: 3.682A pdb=" N SER B 320 " --> pdb=" O LYS B 316 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR B 337 " --> pdb=" O ILE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 402 removed outlier: 3.650A pdb=" N LYS B 401 " --> pdb=" O LYS B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 423 Processing helix chain 'B' and resid 423 through 436 removed outlier: 3.697A pdb=" N LEU B 430 " --> pdb=" O ASN B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 458 Processing helix chain 'B' and resid 472 through 483 Processing helix chain 'B' and resid 485 through 489 Processing helix chain 'B' and resid 499 through 503 Processing helix chain 'B' and resid 506 through 517 Processing helix chain 'B' and resid 517 through 523 Processing helix chain 'B' and resid 523 through 531 removed outlier: 3.504A pdb=" N PHE B 527 " --> pdb=" O ASN B 523 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 559 Processing helix chain 'B' and resid 577 through 593 Processing helix chain 'B' and resid 603 through 606 Processing helix chain 'B' and resid 618 through 630 Processing helix chain 'B' and resid 646 through 650 Processing helix chain 'B' and resid 670 through 684 removed outlier: 3.834A pdb=" N VAL B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS B 676 " --> pdb=" O GLU B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 725 Processing helix chain 'B' and resid 726 through 729 Processing helix chain 'B' and resid 732 through 761 Processing helix chain 'B' and resid 776 through 784 removed outlier: 3.521A pdb=" N TRP B 780 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B 782 " --> pdb=" O GLU B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 798 Processing helix chain 'C' and resid 200 through 204 removed outlier: 3.533A pdb=" N ILE C 204 " --> pdb=" O ILE C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 218 removed outlier: 4.089A pdb=" N LYS C 216 " --> pdb=" O GLN C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 224 removed outlier: 3.511A pdb=" N LEU C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 231 removed outlier: 3.524A pdb=" N CYS C 228 " --> pdb=" O GLY C 224 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET C 231 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 259 removed outlier: 3.507A pdb=" N GLY C 258 " --> pdb=" O HIS C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 273 Processing helix chain 'C' and resid 278 through 294 removed outlier: 3.697A pdb=" N ILE C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 307 Processing helix chain 'C' and resid 317 through 337 removed outlier: 4.173A pdb=" N ARG C 334 " --> pdb=" O MET C 330 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN C 335 " --> pdb=" O ASP C 331 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR C 337 " --> pdb=" O ILE C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 355 Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 373 through 385 removed outlier: 3.506A pdb=" N GLN C 379 " --> pdb=" O ARG C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 407 through 423 Processing helix chain 'C' and resid 424 through 436 removed outlier: 3.572A pdb=" N LEU C 430 " --> pdb=" O ASN C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 459 Processing helix chain 'C' and resid 472 through 483 removed outlier: 3.903A pdb=" N SER C 481 " --> pdb=" O ARG C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 489 Processing helix chain 'C' and resid 499 through 503 Processing helix chain 'C' and resid 506 through 517 Processing helix chain 'C' and resid 517 through 523 Processing helix chain 'C' and resid 523 through 530 removed outlier: 3.785A pdb=" N PHE C 527 " --> pdb=" O ASN C 523 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL C 530 " --> pdb=" O LEU C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 559 Processing helix chain 'C' and resid 577 through 593 Processing helix chain 'C' and resid 603 through 606 Processing helix chain 'C' and resid 615 through 630 removed outlier: 3.868A pdb=" N VAL C 621 " --> pdb=" O ALA C 617 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 622 " --> pdb=" O SER C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 650 Processing helix chain 'C' and resid 670 through 684 removed outlier: 3.649A pdb=" N VAL C 675 " --> pdb=" O ALA C 671 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS C 676 " --> pdb=" O GLU C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 725 Processing helix chain 'C' and resid 726 through 729 Processing helix chain 'C' and resid 732 through 761 Processing helix chain 'C' and resid 776 through 785 removed outlier: 3.572A pdb=" N LYS C 782 " --> pdb=" O GLU C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 799 removed outlier: 4.167A pdb=" N TYR C 797 " --> pdb=" O ASP C 793 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS C 799 " --> pdb=" O GLU C 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'D' and resid 207 through 218 removed outlier: 3.662A pdb=" N LEU D 211 " --> pdb=" O VAL D 207 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS D 216 " --> pdb=" O GLN D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 224 through 232 Processing helix chain 'D' and resid 248 through 261 removed outlier: 3.527A pdb=" N GLY D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 removed outlier: 4.238A pdb=" N ILE D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 269 through 273' Processing helix chain 'D' and resid 278 through 294 removed outlier: 3.609A pdb=" N ILE D 284 " --> pdb=" O SER D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 307 Processing helix chain 'D' and resid 317 through 337 removed outlier: 3.526A pdb=" N ILE D 333 " --> pdb=" O GLY D 329 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ARG D 334 " --> pdb=" O MET D 330 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN D 335 " --> pdb=" O ASP D 331 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR D 337 " --> pdb=" O ILE D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'D' and resid 356 through 361 Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 407 through 423 Processing helix chain 'D' and resid 424 through 435 removed outlier: 3.679A pdb=" N LEU D 430 " --> pdb=" O ASN D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 460 Processing helix chain 'D' and resid 472 through 483 removed outlier: 3.554A pdb=" N SER D 481 " --> pdb=" O ARG D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 489 removed outlier: 3.625A pdb=" N ARG D 489 " --> pdb=" O ALA D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 503 Processing helix chain 'D' and resid 506 through 517 Processing helix chain 'D' and resid 517 through 523 Processing helix chain 'D' and resid 523 through 530 removed outlier: 3.895A pdb=" N VAL D 530 " --> pdb=" O LEU D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.514A pdb=" N VAL D 555 " --> pdb=" O VAL D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 593 removed outlier: 3.603A pdb=" N VAL D 583 " --> pdb=" O SER D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 606 Processing helix chain 'D' and resid 618 through 630 Processing helix chain 'D' and resid 646 through 650 Processing helix chain 'D' and resid 670 through 684 removed outlier: 3.737A pdb=" N VAL D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS D 676 " --> pdb=" O GLU D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 725 removed outlier: 3.561A pdb=" N GLU D 720 " --> pdb=" O ASP D 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 726 through 729 Processing helix chain 'D' and resid 732 through 754 Processing helix chain 'D' and resid 776 through 787 removed outlier: 3.910A pdb=" N ASN D 785 " --> pdb=" O GLU D 781 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU D 786 " --> pdb=" O LYS D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 799 removed outlier: 3.722A pdb=" N HIS D 799 " --> pdb=" O GLU D 795 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 204 Processing helix chain 'E' and resid 207 through 218 removed outlier: 3.727A pdb=" N LEU E 215 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS E 216 " --> pdb=" O GLN E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 224 removed outlier: 3.550A pdb=" N LEU E 222 " --> pdb=" O VAL E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 232 removed outlier: 4.187A pdb=" N CYS E 228 " --> pdb=" O GLY E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 261 removed outlier: 3.717A pdb=" N GLY E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 272 No H-bonds generated for 'chain 'E' and resid 270 through 272' Processing helix chain 'E' and resid 278 through 294 Processing helix chain 'E' and resid 303 through 307 Processing helix chain 'E' and resid 316 through 336 Processing helix chain 'E' and resid 351 through 355 Processing helix chain 'E' and resid 356 through 362 removed outlier: 3.849A pdb=" N ARG E 362 " --> pdb=" O ALA E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 402 removed outlier: 3.849A pdb=" N LEU E 399 " --> pdb=" O ASN E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 422 Processing helix chain 'E' and resid 472 through 483 removed outlier: 3.738A pdb=" N PHE E 476 " --> pdb=" O THR E 472 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER E 481 " --> pdb=" O ARG E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 503 Processing helix chain 'E' and resid 506 through 517 removed outlier: 3.550A pdb=" N MET E 515 " --> pdb=" O LYS E 511 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 523 removed outlier: 3.517A pdb=" N LYS E 522 " --> pdb=" O ILE E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 530 removed outlier: 3.639A pdb=" N VAL E 530 " --> pdb=" O LEU E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 560 Processing helix chain 'E' and resid 568 through 572 Processing helix chain 'E' and resid 577 through 593 removed outlier: 3.731A pdb=" N VAL E 583 " --> pdb=" O SER E 579 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE E 587 " --> pdb=" O VAL E 583 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER E 588 " --> pdb=" O ARG E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 603 through 606 Processing helix chain 'E' and resid 616 through 629 removed outlier: 3.631A pdb=" N VAL E 621 " --> pdb=" O ALA E 617 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL E 622 " --> pdb=" O SER E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 632 No H-bonds generated for 'chain 'E' and resid 630 through 632' Processing helix chain 'E' and resid 646 through 650 removed outlier: 3.846A pdb=" N ILE E 650 " --> pdb=" O PRO E 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 651 through 656 removed outlier: 3.704A pdb=" N ARG E 656 " --> pdb=" O ALA E 653 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 683 Processing helix chain 'E' and resid 716 through 724 removed outlier: 3.598A pdb=" N VAL E 722 " --> pdb=" O ASP E 718 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA E 723 " --> pdb=" O LEU E 719 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 750 removed outlier: 3.851A pdb=" N GLY E 737 " --> pdb=" O GLY E 733 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN E 741 " --> pdb=" O GLY E 737 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA E 746 " --> pdb=" O ALA E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 777 through 785 removed outlier: 4.255A pdb=" N GLU E 781 " --> pdb=" O MET E 777 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS E 782 " --> pdb=" O GLU E 778 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA E 783 " --> pdb=" O ASP E 779 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN E 785 " --> pdb=" O GLU E 781 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 385 removed outlier: 4.243A pdb=" N GLN F 379 " --> pdb=" O ARG F 375 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE F 380 " --> pdb=" O ALA F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 402 removed outlier: 3.522A pdb=" N MET F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 436 removed outlier: 3.889A pdb=" N TYR F 413 " --> pdb=" O SER F 409 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA F 425 " --> pdb=" O GLU F 421 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN F 426 " --> pdb=" O SER F 422 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA F 436 " --> pdb=" O ALA F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 460 removed outlier: 3.959A pdb=" N HIS F 459 " --> pdb=" O LEU F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 483 removed outlier: 3.560A pdb=" N SER F 481 " --> pdb=" O ARG F 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 485 through 489 Processing helix chain 'F' and resid 506 through 517 removed outlier: 3.980A pdb=" N LYS F 511 " --> pdb=" O GLU F 507 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS F 512 " --> pdb=" O ASP F 508 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N MET F 515 " --> pdb=" O LYS F 511 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 523 removed outlier: 3.996A pdb=" N LYS F 522 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN F 523 " --> pdb=" O GLY F 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 518 through 523' Processing helix chain 'F' and resid 526 through 531 Processing helix chain 'F' and resid 547 through 559 Processing helix chain 'F' and resid 567 through 572 Processing helix chain 'F' and resid 580 through 593 removed outlier: 3.549A pdb=" N ARG F 584 " --> pdb=" O GLU F 580 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE F 587 " --> pdb=" O VAL F 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 602 through 606 Processing helix chain 'F' and resid 620 through 631 removed outlier: 3.680A pdb=" N LEU F 626 " --> pdb=" O VAL F 622 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU F 628 " --> pdb=" O THR F 624 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP F 630 " --> pdb=" O LEU F 626 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLY F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 670 through 685 removed outlier: 4.002A pdb=" N LYS F 676 " --> pdb=" O GLU F 672 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU F 681 " --> pdb=" O ILE F 677 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASN F 684 " --> pdb=" O THR F 680 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR F 685 " --> pdb=" O LEU F 681 " (cutoff:3.500A) Processing helix chain 'F' and resid 718 through 723 removed outlier: 3.762A pdb=" N ALA F 723 " --> pdb=" O LEU F 719 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 754 removed outlier: 3.583A pdb=" N GLY F 737 " --> pdb=" O GLY F 733 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN F 738 " --> pdb=" O ALA F 734 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU F 739 " --> pdb=" O ASP F 735 " (cutoff:3.500A) Processing helix chain 'F' and resid 776 through 785 removed outlier: 3.552A pdb=" N TRP F 780 " --> pdb=" O THR F 776 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS F 782 " --> pdb=" O GLU F 778 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA F 783 " --> pdb=" O ASP F 779 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASN F 785 " --> pdb=" O GLU F 781 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.630A pdb=" N ALA A 263 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N PHE A 300 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE A 265 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASP A 302 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A 267 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N CYS A 297 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU A 346 " --> pdb=" O CYS A 297 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE A 299 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ALA A 348 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU A 301 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU A 240 " --> pdb=" O ILE A 367 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 562 through 567 removed outlier: 6.531A pdb=" N CYS A 596 " --> pdb=" O TYR A 639 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE A 641 " --> pdb=" O CYS A 596 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU A 598 " --> pdb=" O ILE A 641 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ALA A 643 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE A 600 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 536 " --> pdb=" O ILE A 638 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 263 through 268 removed outlier: 6.655A pdb=" N ALA B 263 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHE B 300 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE B 265 " --> pdb=" O PHE B 300 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ASP B 302 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 267 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N CYS B 297 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU B 346 " --> pdb=" O CYS B 297 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ILE B 299 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ALA B 348 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU B 301 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 562 through 567 removed outlier: 6.305A pdb=" N CYS B 596 " --> pdb=" O TYR B 639 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE B 641 " --> pdb=" O CYS B 596 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU B 598 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ALA B 643 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE B 600 " --> pdb=" O ALA B 643 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA B 536 " --> pdb=" O ILE B 638 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 263 through 268 removed outlier: 6.391A pdb=" N CYS C 297 " --> pdb=" O VAL C 344 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU C 346 " --> pdb=" O CYS C 297 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE C 299 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ALA C 348 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU C 301 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLY C 238 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE C 367 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU C 240 " --> pdb=" O ILE C 367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 562 through 567 removed outlier: 6.322A pdb=" N CYS C 596 " --> pdb=" O TYR C 639 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE C 641 " --> pdb=" O CYS C 596 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU C 598 " --> pdb=" O ILE C 641 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ALA C 643 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE C 600 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA C 536 " --> pdb=" O ILE C 638 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLY C 537 " --> pdb=" O THR C 662 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE C 664 " --> pdb=" O GLY C 537 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU C 539 " --> pdb=" O ILE C 664 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 263 through 268 removed outlier: 6.487A pdb=" N CYS D 297 " --> pdb=" O VAL D 344 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU D 346 " --> pdb=" O CYS D 297 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE D 299 " --> pdb=" O LEU D 346 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA D 348 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU D 301 " --> pdb=" O ALA D 348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 562 through 567 removed outlier: 6.352A pdb=" N CYS D 596 " --> pdb=" O TYR D 639 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ILE D 641 " --> pdb=" O CYS D 596 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU D 598 " --> pdb=" O ILE D 641 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ALA D 643 " --> pdb=" O LEU D 598 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE D 600 " --> pdb=" O ALA D 643 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLY D 537 " --> pdb=" O THR D 662 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE D 664 " --> pdb=" O GLY D 537 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU D 539 " --> pdb=" O ILE D 664 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 263 through 268 removed outlier: 6.369A pdb=" N CYS E 297 " --> pdb=" O VAL E 344 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU E 346 " --> pdb=" O CYS E 297 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE E 299 " --> pdb=" O LEU E 346 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ALA E 348 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU E 301 " --> pdb=" O ALA E 348 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 562 through 566 removed outlier: 6.472A pdb=" N ASN E 562 " --> pdb=" O ILE E 597 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N PHE E 599 " --> pdb=" O ASN E 562 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE E 564 " --> pdb=" O PHE E 599 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ASP E 601 " --> pdb=" O ILE E 564 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE E 566 " --> pdb=" O ASP E 601 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE E 538 " --> pdb=" O GLY E 642 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N THR E 644 " --> pdb=" O ILE E 538 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU E 540 " --> pdb=" O THR E 644 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N THR E 662 " --> pdb=" O GLY E 537 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 492 through 493 removed outlier: 6.386A pdb=" N ASN F 562 " --> pdb=" O ILE F 597 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE F 599 " --> pdb=" O ASN F 562 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE F 564 " --> pdb=" O PHE F 599 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N CYS F 596 " --> pdb=" O TYR F 639 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE F 641 " --> pdb=" O CYS F 596 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU F 598 " --> pdb=" O ILE F 641 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA F 643 " --> pdb=" O LEU F 598 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE F 600 " --> pdb=" O ALA F 643 " (cutoff:3.500A) 1172 hydrogen bonds defined for protein. 3272 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: 9.42 Time building geometry restraints manager: 7.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8024 1.34 - 1.46: 4124 1.46 - 1.58: 11891 1.58 - 1.69: 48 1.69 - 1.81: 192 Bond restraints: 24279 Sorted by residual: bond pdb=" O5' ATP E 902 " pdb=" PA ATP E 902 " ideal model delta sigma weight residual 1.579 1.610 -0.031 1.10e-02 8.26e+03 7.98e+00 bond pdb=" O5' ATP A 901 " pdb=" PA ATP A 901 " ideal model delta sigma weight residual 1.579 1.609 -0.030 1.10e-02 8.26e+03 7.43e+00 bond pdb=" O5' ATP A 902 " pdb=" PA ATP A 902 " ideal model delta sigma weight residual 1.579 1.609 -0.030 1.10e-02 8.26e+03 7.36e+00 bond pdb=" O5' ATP D 901 " pdb=" PA ATP D 901 " ideal model delta sigma weight residual 1.579 1.609 -0.030 1.10e-02 8.26e+03 7.33e+00 bond pdb=" O5' ATP B 901 " pdb=" PA ATP B 901 " ideal model delta sigma weight residual 1.579 1.609 -0.030 1.10e-02 8.26e+03 7.24e+00 ... (remaining 24274 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 32534 2.09 - 4.18: 271 4.18 - 6.27: 49 6.27 - 8.36: 12 8.36 - 10.45: 7 Bond angle restraints: 32873 Sorted by residual: angle pdb=" PB ATP E 902 " pdb=" O3B ATP E 902 " pdb=" PG ATP E 902 " ideal model delta sigma weight residual 139.87 129.42 10.45 1.00e+00 1.00e+00 1.09e+02 angle pdb=" PB ATP B 901 " pdb=" O3B ATP B 901 " pdb=" PG ATP B 901 " ideal model delta sigma weight residual 139.87 129.59 10.28 1.00e+00 1.00e+00 1.06e+02 angle pdb=" PB ATP B 902 " pdb=" O3B ATP B 902 " pdb=" PG ATP B 902 " ideal model delta sigma weight residual 139.87 129.89 9.98 1.00e+00 1.00e+00 9.95e+01 angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 130.23 9.64 1.00e+00 1.00e+00 9.30e+01 angle pdb=" PB ATP D 902 " pdb=" O3B ATP D 902 " pdb=" PG ATP D 902 " ideal model delta sigma weight residual 139.87 130.92 8.95 1.00e+00 1.00e+00 8.01e+01 ... (remaining 32868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.83: 14690 24.83 - 49.65: 329 49.65 - 74.48: 85 74.48 - 99.31: 9 99.31 - 124.13: 1 Dihedral angle restraints: 15114 sinusoidal: 6318 harmonic: 8796 Sorted by residual: dihedral pdb=" C5' ADP E 901 " pdb=" O5' ADP E 901 " pdb=" PA ADP E 901 " pdb=" O2A ADP E 901 " ideal model delta sinusoidal sigma weight residual 300.00 175.87 124.13 1 2.00e+01 2.50e-03 3.75e+01 dihedral pdb=" O2A ADP E 901 " pdb=" O3A ADP E 901 " pdb=" PA ADP E 901 " pdb=" PB ADP E 901 " ideal model delta sinusoidal sigma weight residual -60.00 -134.83 74.83 1 2.00e+01 2.50e-03 1.77e+01 dihedral pdb=" CA ARG D 635 " pdb=" CB ARG D 635 " pdb=" CG ARG D 635 " pdb=" CD ARG D 635 " ideal model delta sinusoidal sigma weight residual 60.00 118.64 -58.64 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 15111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2259 0.029 - 0.058: 1036 0.058 - 0.087: 220 0.087 - 0.116: 211 0.116 - 0.144: 36 Chirality restraints: 3762 Sorted by residual: chirality pdb=" C3' ATP D 902 " pdb=" C2' ATP D 902 " pdb=" C4' ATP D 902 " pdb=" O3' ATP D 902 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" C3' ATP E 902 " pdb=" C2' ATP E 902 " pdb=" C4' ATP E 902 " pdb=" O3' ATP E 902 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" C3' ATP A 901 " pdb=" C2' ATP A 901 " pdb=" C4' ATP A 901 " pdb=" O3' ATP A 901 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 3759 not shown) Planarity restraints: 4214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 356 " 0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO A 357 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 357 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 357 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 519 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.43e+00 pdb=" N PRO A 520 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 520 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 520 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 220 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO D 221 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 221 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 221 " -0.016 5.00e-02 4.00e+02 ... (remaining 4211 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 172 2.54 - 3.13: 18071 3.13 - 3.72: 36542 3.72 - 4.31: 53475 4.31 - 4.90: 89334 Nonbonded interactions: 197594 Sorted by model distance: nonbonded pdb=" O1B ATP B 901 " pdb="MG MG B 903 " model vdw 1.953 2.170 nonbonded pdb=" O1B ATP C 902 " pdb="MG MG C 904 " model vdw 1.970 2.170 nonbonded pdb=" O1B ATP D 902 " pdb="MG MG D 904 " model vdw 1.993 2.170 nonbonded pdb=" O2G ATP D 901 " pdb="MG MG D 903 " model vdw 1.994 2.170 nonbonded pdb=" O2G ATP C 902 " pdb="MG MG C 904 " model vdw 1.995 2.170 ... (remaining 197589 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 200 through 302 or resid 304 through 388 or resid 394 thro \ ugh 425 or resid 470 through 483 or (resid 484 and (name N or name CA or name C \ or name O or name CB )) or resid 485 through 487 or resid 494 through 588 or res \ id 590 through 634 or (resid 635 and (name N or name CA or name C or name O or n \ ame CB )) or resid 636 through 654 or resid 656 through 726 or resid 732 through \ 751 or resid 775 through 788 or resid 904)) selection = (chain 'B' and (resid 200 through 302 or resid 304 through 309 or resid 317 thro \ ugh 388 or resid 394 through 425 or resid 470 through 483 or (resid 484 and (nam \ e N or name CA or name C or name O or name CB )) or resid 485 through 487 or res \ id 494 through 588 or resid 590 through 634 or (resid 635 and (name N or name CA \ or name C or name O or name CB )) or resid 636 through 654 or resid 656 through \ 726 or resid 732 through 751 or resid 775 through 788 or resid 904)) selection = (chain 'C' and (resid 200 through 302 or resid 304 through 309 or resid 317 thro \ ugh 388 or resid 394 through 425 or resid 470 through 483 or (resid 484 and (nam \ e N or name CA or name C or name O or name CB )) or resid 485 through 487 or res \ id 494 through 588 or resid 590 through 634 or (resid 635 and (name N or name CA \ or name C or name O or name CB )) or resid 636 through 654 or resid 656 through \ 726 or resid 732 through 751 or resid 775 through 788 or resid 904)) selection = (chain 'D' and (resid 200 through 302 or resid 304 through 309 or resid 317 thro \ ugh 388 or resid 394 through 425 or resid 470 through 483 or (resid 484 and (nam \ e N or name CA or name C or name O or name CB )) or resid 485 through 487 or res \ id 494 through 588 or resid 590 through 634 or (resid 635 and (name N or name CA \ or name C or name O or name CB )) or resid 636 through 654 or resid 656 through \ 726 or resid 732 through 751 or resid 775 through 788 or resid 904)) selection = (chain 'E' and (resid 200 through 302 or resid 304 through 309 or resid 317 thro \ ugh 588 or resid 590 through 654 or resid 656 through 788 or resid 903)) } 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=0.40 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: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.000 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 65.540 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.140 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:25.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 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 : 0.003 0.053 24279 Z= 0.152 Angle : 0.509 10.455 32873 Z= 0.305 Chirality : 0.040 0.144 3762 Planarity : 0.003 0.035 4214 Dihedral : 11.234 124.134 9416 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.00 % Favored : 96.94 % Rotamer: Outliers : 0.95 % Allowed : 2.88 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.16), residues: 3006 helix: -0.21 (0.13), residues: 1583 sheet: 0.79 (0.28), residues: 365 loop : 0.65 (0.21), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 541 HIS 0.003 0.001 HIS C 242 PHE 0.008 0.001 PHE C 264 TYR 0.009 0.001 TYR B 406 ARG 0.003 0.000 ARG C 377 Details of bonding type rmsd hydrogen bonds : bond 0.27120 ( 1172) hydrogen bonds : angle 7.44932 ( 3272) covalent geometry : bond 0.00323 (24279) covalent geometry : angle 0.50948 (32873) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 541 time to evaluate : 2.706 Fit side-chains TARDY: cannot create tardy model for: "MET B 199 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET C 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 199 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 204 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8647 (tp) REVERT: A 208 ASP cc_start: 0.7875 (m-30) cc_final: 0.7465 (m-30) REVERT: A 401 LYS cc_start: 0.8407 (mtmt) cc_final: 0.8180 (tptt) REVERT: A 735 ASP cc_start: 0.8623 (m-30) cc_final: 0.8321 (m-30) REVERT: B 351 ARG cc_start: 0.7899 (mmt-90) cc_final: 0.7691 (mmt90) REVERT: B 649 MET cc_start: 0.8070 (mmm) cc_final: 0.7754 (mmp) REVERT: B 777 MET cc_start: 0.8479 (tpt) cc_final: 0.8260 (tpt) REVERT: C 286 ASP cc_start: 0.7882 (m-30) cc_final: 0.7607 (m-30) REVERT: C 635 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7989 (ppt170) REVERT: C 757 GLN cc_start: 0.6926 (tt0) cc_final: 0.6534 (mt0) REVERT: D 401 LYS cc_start: 0.8520 (mtmt) cc_final: 0.8220 (tttp) REVERT: D 778 GLU cc_start: 0.8054 (pt0) cc_final: 0.7683 (tp30) REVERT: E 416 LYS cc_start: 0.7499 (mttt) cc_final: 0.7083 (mmtt) REVERT: E 472 THR cc_start: 0.7282 (OUTLIER) cc_final: 0.7080 (t) REVERT: E 473 MET cc_start: 0.6010 (tmm) cc_final: 0.5747 (ppp) REVERT: E 475 GLN cc_start: 0.6054 (mt0) cc_final: 0.5675 (mt0) REVERT: E 526 LEU cc_start: 0.8078 (tp) cc_final: 0.7530 (tp) REVERT: E 639 TYR cc_start: 0.7789 (m-80) cc_final: 0.7388 (m-80) REVERT: E 776 THR cc_start: 0.6000 (p) cc_final: 0.5736 (t) REVERT: F 424 GLN cc_start: 0.7342 (tp40) cc_final: 0.6571 (tt0) REVERT: F 586 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7038 (mp) REVERT: F 601 ASP cc_start: 0.6872 (p0) cc_final: 0.6355 (t0) REVERT: F 649 MET cc_start: 0.6171 (mmm) cc_final: 0.5468 (mmm) REVERT: F 754 GLN cc_start: 0.6943 (mt0) cc_final: 0.6285 (pp30) REVERT: F 782 LYS cc_start: 0.6716 (ptpp) cc_final: 0.6147 (tttp) outliers start: 24 outliers final: 7 residues processed: 559 average time/residue: 1.6567 time to fit residues: 1041.2714 Evaluate side-chains 339 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 328 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 771 ILE Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain F residue 476 PHE Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain G residue 18 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 5.9990 chunk 230 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 123 optimal weight: 50.0000 chunk 238 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 144 optimal weight: 0.4980 chunk 177 optimal weight: 7.9990 chunk 276 optimal weight: 50.0000 overall best weight: 3.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 585 GLN ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 GLN C 424 GLN C 562 ASN C 585 GLN D 433 GLN D 741 GLN E 335 GLN E 523 ASN E 602 GLN ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 745 GLN F 433 GLN F 450 GLN F 484 GLN F 785 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.169295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.129265 restraints weight = 53873.013| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 4.14 r_work: 0.3115 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24279 Z= 0.160 Angle : 0.580 9.167 32873 Z= 0.298 Chirality : 0.044 0.273 3762 Planarity : 0.005 0.055 4214 Dihedral : 11.571 103.588 3662 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.33 % Favored : 96.64 % Rotamer: Outliers : 2.52 % Allowed : 10.92 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.16), residues: 3006 helix: 0.51 (0.13), residues: 1612 sheet: 0.47 (0.27), residues: 382 loop : 0.72 (0.22), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 219 HIS 0.003 0.001 HIS D 254 PHE 0.022 0.002 PHE E 527 TYR 0.013 0.001 TYR A 752 ARG 0.007 0.001 ARG B 609 Details of bonding type rmsd hydrogen bonds : bond 0.05575 ( 1172) hydrogen bonds : angle 4.85084 ( 3272) covalent geometry : bond 0.00366 (24279) covalent geometry : angle 0.57974 (32873) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 382 time to evaluate : 4.613 Fit side-chains TARDY: cannot create tardy model for: "MET B 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 199 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 204 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8415 (mp) REVERT: A 223 ARG cc_start: 0.6381 (tpm170) cc_final: 0.6159 (tpt170) REVERT: A 234 ARG cc_start: 0.6322 (ttm110) cc_final: 0.5998 (ttm110) REVERT: A 351 ARG cc_start: 0.7374 (mmp-170) cc_final: 0.6642 (tpp-160) REVERT: A 401 LYS cc_start: 0.8658 (mtmt) cc_final: 0.8242 (tptt) REVERT: A 490 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8238 (tt0) REVERT: A 560 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8824 (mttp) REVERT: A 716 ASP cc_start: 0.7956 (t0) cc_final: 0.7106 (m-30) REVERT: A 735 ASP cc_start: 0.9050 (m-30) cc_final: 0.8710 (m-30) REVERT: A 795 GLU cc_start: 0.7260 (pp20) cc_final: 0.7001 (pp20) REVERT: A 796 LYS cc_start: 0.5584 (tmtp) cc_final: 0.4920 (mmpt) REVERT: B 320 SER cc_start: 0.8560 (t) cc_final: 0.8323 (m) REVERT: B 325 GLU cc_start: 0.8152 (tp30) cc_final: 0.7668 (tp30) REVERT: B 335 GLN cc_start: 0.8144 (mt0) cc_final: 0.7924 (mt0) REVERT: B 433 GLN cc_start: 0.7800 (tp40) cc_final: 0.7370 (tm-30) REVERT: B 618 SER cc_start: 0.8154 (OUTLIER) cc_final: 0.7901 (p) REVERT: B 755 ARG cc_start: 0.6508 (ttp-170) cc_final: 0.6292 (ttp80) REVERT: B 777 MET cc_start: 0.8810 (tpt) cc_final: 0.8557 (tpt) REVERT: C 286 ASP cc_start: 0.8255 (m-30) cc_final: 0.7794 (m-30) REVERT: C 635 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8614 (ppt-90) REVERT: C 757 GLN cc_start: 0.6759 (tt0) cc_final: 0.6393 (mt0) REVERT: D 234 ARG cc_start: 0.7813 (ttm110) cc_final: 0.7580 (ttm110) REVERT: D 533 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8136 (mptp) REVERT: D 778 GLU cc_start: 0.8433 (pt0) cc_final: 0.7534 (tp30) REVERT: D 781 GLU cc_start: 0.7579 (mp0) cc_final: 0.7048 (mp0) REVERT: E 223 ARG cc_start: 0.8090 (tpm170) cc_final: 0.7850 (mmt-90) REVERT: E 282 LYS cc_start: 0.7615 (tttt) cc_final: 0.7134 (tmtm) REVERT: E 318 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.7099 (ttt) REVERT: E 416 LYS cc_start: 0.7045 (mttt) cc_final: 0.6632 (mmtm) REVERT: E 472 THR cc_start: 0.7101 (OUTLIER) cc_final: 0.6707 (t) REVERT: E 475 GLN cc_start: 0.5408 (mt0) cc_final: 0.5087 (mm-40) REVERT: E 478 LYS cc_start: 0.6607 (tptp) cc_final: 0.6283 (mmtp) REVERT: E 515 MET cc_start: 0.8403 (ttp) cc_final: 0.8114 (tpp) REVERT: E 567 LYS cc_start: 0.7874 (tptp) cc_final: 0.7650 (tptp) REVERT: E 741 GLN cc_start: 0.7018 (OUTLIER) cc_final: 0.6370 (tt0) REVERT: F 424 GLN cc_start: 0.7095 (tp40) cc_final: 0.6330 (tt0) REVERT: F 586 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6793 (mp) REVERT: F 601 ASP cc_start: 0.6212 (p0) cc_final: 0.5982 (t0) REVERT: F 604 ASP cc_start: 0.7467 (p0) cc_final: 0.6778 (p0) REVERT: F 740 MET cc_start: 0.7190 (ttp) cc_final: 0.6382 (tmm) REVERT: F 754 GLN cc_start: 0.6823 (mt0) cc_final: 0.6197 (pp30) REVERT: F 786 GLU cc_start: 0.6076 (mp0) cc_final: 0.5199 (mt-10) REVERT: G 17 LEU cc_start: 0.8402 (mp) cc_final: 0.8110 (mp) outliers start: 64 outliers final: 21 residues processed: 417 average time/residue: 1.6329 time to fit residues: 768.1413 Evaluate side-chains 358 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 327 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 771 ILE Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 533 LYS Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 741 GLN Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 673 ASP Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 747 CYS Chi-restraints excluded: chain F residue 774 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 25 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 298 optimal weight: 40.0000 chunk 253 optimal weight: 3.9990 chunk 288 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 259 optimal weight: 20.0000 chunk 41 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 424 GLN ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.168573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.128265 restraints weight = 46548.221| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.75 r_work: 0.3126 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24279 Z= 0.166 Angle : 0.554 7.904 32873 Z= 0.278 Chirality : 0.044 0.187 3762 Planarity : 0.004 0.044 4214 Dihedral : 11.494 92.883 3658 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.46 % Favored : 96.50 % Rotamer: Outliers : 2.72 % Allowed : 11.99 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.16), residues: 3006 helix: 0.68 (0.13), residues: 1614 sheet: 0.25 (0.26), residues: 381 loop : 0.59 (0.22), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 466 HIS 0.004 0.001 HIS C 242 PHE 0.023 0.002 PHE E 527 TYR 0.011 0.001 TYR B 406 ARG 0.008 0.001 ARG B 609 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 1172) hydrogen bonds : angle 4.39013 ( 3272) covalent geometry : bond 0.00401 (24279) covalent geometry : angle 0.55414 (32873) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 356 time to evaluate : 4.638 Fit side-chains TARDY: cannot create tardy model for: "MET B 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 199 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 204 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8420 (mp) REVERT: A 290 GLU cc_start: 0.7411 (tp30) cc_final: 0.7162 (tp30) REVERT: A 351 ARG cc_start: 0.7281 (mmp-170) cc_final: 0.6785 (tpp-160) REVERT: A 371 MET cc_start: 0.8967 (mtt) cc_final: 0.8599 (mtt) REVERT: A 474 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7117 (mm-30) REVERT: A 490 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8211 (tt0) REVERT: A 560 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8942 (mttp) REVERT: A 735 ASP cc_start: 0.9033 (m-30) cc_final: 0.8672 (m-30) REVERT: A 795 GLU cc_start: 0.7403 (pp20) cc_final: 0.7198 (pp20) REVERT: A 796 LYS cc_start: 0.6215 (tmtp) cc_final: 0.5537 (mmpt) REVERT: B 320 SER cc_start: 0.8426 (t) cc_final: 0.8212 (m) REVERT: B 325 GLU cc_start: 0.8138 (tp30) cc_final: 0.7592 (tp30) REVERT: B 335 GLN cc_start: 0.8088 (mt0) cc_final: 0.7813 (mp10) REVERT: B 433 GLN cc_start: 0.7819 (tp40) cc_final: 0.7461 (tm-30) REVERT: B 618 SER cc_start: 0.8215 (OUTLIER) cc_final: 0.7967 (p) REVERT: B 755 ARG cc_start: 0.6528 (ttp-170) cc_final: 0.6311 (ttp80) REVERT: B 777 MET cc_start: 0.8829 (tpt) cc_final: 0.8540 (tpt) REVERT: C 286 ASP cc_start: 0.8112 (m-30) cc_final: 0.7599 (m-30) REVERT: C 635 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8578 (ppt-90) REVERT: C 757 GLN cc_start: 0.6486 (tt0) cc_final: 0.6184 (mt0) REVERT: D 330 MET cc_start: 0.9086 (mtp) cc_final: 0.8798 (mtm) REVERT: D 369 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8273 (mtp) REVERT: D 421 GLU cc_start: 0.7727 (tp30) cc_final: 0.7118 (tp30) REVERT: D 533 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8088 (mptp) REVERT: D 781 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7261 (mp0) REVERT: E 234 ARG cc_start: 0.7611 (mtt90) cc_final: 0.7209 (ttp-110) REVERT: E 282 LYS cc_start: 0.7441 (tttt) cc_final: 0.7108 (tptt) REVERT: E 286 ASP cc_start: 0.7928 (m-30) cc_final: 0.7687 (m-30) REVERT: E 318 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.6976 (ttt) REVERT: E 320 SER cc_start: 0.7600 (t) cc_final: 0.7281 (m) REVERT: E 478 LYS cc_start: 0.6596 (tptp) cc_final: 0.6187 (mmtp) REVERT: E 507 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6395 (tm-30) REVERT: E 526 LEU cc_start: 0.8031 (tp) cc_final: 0.7816 (tp) REVERT: E 585 GLN cc_start: 0.8283 (tt0) cc_final: 0.8025 (mm-40) REVERT: E 602 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7573 (tt0) REVERT: E 639 TYR cc_start: 0.8266 (m-80) cc_final: 0.7951 (m-80) REVERT: E 646 ARG cc_start: 0.7783 (mtp180) cc_final: 0.7505 (mtp-110) REVERT: E 741 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6379 (tt0) REVERT: F 424 GLN cc_start: 0.7101 (tp40) cc_final: 0.6278 (tt0) REVERT: F 539 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6935 (tm) REVERT: F 586 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6859 (mp) REVERT: F 603 MET cc_start: 0.6384 (OUTLIER) cc_final: 0.6025 (ptp) REVERT: F 740 MET cc_start: 0.7289 (ttp) cc_final: 0.6903 (tmm) REVERT: F 754 GLN cc_start: 0.6855 (mt0) cc_final: 0.6189 (pt0) REVERT: G 17 LEU cc_start: 0.8363 (mp) cc_final: 0.8019 (mp) outliers start: 69 outliers final: 26 residues processed: 395 average time/residue: 2.0828 time to fit residues: 927.4526 Evaluate side-chains 360 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 320 time to evaluate : 2.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain D residue 361 ARG Chi-restraints excluded: chain D residue 369 MET Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 533 LYS Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 507 GLU Chi-restraints excluded: chain E residue 741 GLN Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 603 MET Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 673 ASP Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 774 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 25 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.9859 > 50: distance: 38 - 43: 8.472 distance: 43 - 44: 11.362 distance: 44 - 45: 39.730 distance: 44 - 47: 32.842 distance: 45 - 46: 33.326 distance: 45 - 51: 29.166 distance: 47 - 48: 32.251 distance: 48 - 49: 36.115 distance: 48 - 50: 22.858 distance: 51 - 52: 18.219 distance: 52 - 53: 8.883 distance: 52 - 55: 38.570 distance: 53 - 54: 17.841 distance: 53 - 60: 21.583 distance: 55 - 56: 26.801 distance: 56 - 57: 14.091 distance: 57 - 58: 20.125 distance: 58 - 59: 20.932 distance: 60 - 61: 24.614 distance: 61 - 62: 20.659 distance: 61 - 64: 12.282 distance: 62 - 63: 25.359 distance: 62 - 72: 16.094 distance: 64 - 65: 27.094 distance: 65 - 66: 7.017 distance: 65 - 67: 5.462 distance: 66 - 68: 15.226 distance: 67 - 69: 19.744 distance: 68 - 70: 5.875 distance: 69 - 70: 13.055 distance: 70 - 71: 14.977 distance: 72 - 73: 29.760 distance: 73 - 74: 14.149 distance: 73 - 76: 29.074 distance: 74 - 75: 11.975 distance: 74 - 79: 20.188 distance: 76 - 77: 43.413 distance: 76 - 78: 27.313 distance: 79 - 80: 50.618 distance: 80 - 81: 29.333 distance: 81 - 82: 12.664 distance: 81 - 83: 18.755 distance: 82 - 107: 44.731 distance: 83 - 84: 15.733 distance: 84 - 85: 8.056 distance: 84 - 87: 15.591 distance: 85 - 86: 12.396 distance: 85 - 92: 12.579 distance: 86 - 118: 16.090 distance: 87 - 88: 20.774 distance: 88 - 89: 5.268 distance: 89 - 90: 9.899 distance: 89 - 91: 9.975 distance: 92 - 93: 24.423 distance: 93 - 94: 11.662 distance: 93 - 96: 22.946 distance: 94 - 95: 17.686 distance: 94 - 98: 28.094 distance: 96 - 97: 19.535 distance: 98 - 99: 21.971 distance: 99 - 100: 10.723 distance: 99 - 102: 12.523 distance: 100 - 101: 13.428 distance: 100 - 107: 16.307 distance: 101 - 130: 16.258 distance: 102 - 103: 21.035 distance: 103 - 104: 17.959 distance: 104 - 105: 24.452 distance: 104 - 106: 22.138 distance: 107 - 108: 18.286 distance: 108 - 109: 4.937 distance: 108 - 111: 12.273 distance: 109 - 110: 22.597 distance: 109 - 118: 16.657 distance: 110 - 141: 9.642 distance: 111 - 112: 16.131 distance: 112 - 113: 23.359 distance: 113 - 114: 20.929 distance: 114 - 115: 3.591 distance: 115 - 116: 11.528 distance: 115 - 117: 7.432 distance: 118 - 119: 4.826 distance: 119 - 120: 3.067 distance: 119 - 122: 5.768 distance: 120 - 121: 4.251 distance: 120 - 123: 3.108 distance: 121 - 149: 6.160