Starting phenix.real_space_refine on Sun Jun 30 02:38:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8can_16531/06_2024/8can_16531.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8can_16531/06_2024/8can_16531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8can_16531/06_2024/8can_16531.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8can_16531/06_2024/8can_16531.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8can_16531/06_2024/8can_16531.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8can_16531/06_2024/8can_16531.pdb" } resolution = 1.93 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= 0.010 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: 7 Type Number sf(0) Gaussians Cu 24 5.60 5 S 396 5.16 5 Na 3 4.78 5 C 21840 2.51 5 N 5754 2.21 5 O 9278 1.98 5 H 33930 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 676": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 676": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 676": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 676": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 676": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 676": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 71225 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 11314 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 683, 11275 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 656} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 683, 11275 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 656} Chain breaks: 3 bond proxies already assigned to first conformer: 11367 Chain: "B" Number of atoms: 11314 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 683, 11275 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 656} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 683, 11275 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 656} Chain breaks: 3 bond proxies already assigned to first conformer: 11367 Chain: "C" Number of atoms: 11314 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 683, 11275 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 656} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 683, 11275 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 656} Chain breaks: 3 bond proxies already assigned to first conformer: 11367 Chain: "D" Number of atoms: 11314 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 683, 11275 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 656} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 683, 11275 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 656} Chain breaks: 3 bond proxies already assigned to first conformer: 11367 Chain: "E" Number of atoms: 11314 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 683, 11275 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 656} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 683, 11275 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 656} Chain breaks: 3 bond proxies already assigned to first conformer: 11367 Chain: "F" Number of atoms: 11314 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 683, 11275 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 656} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 683, 11275 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 656} Chain breaks: 3 bond proxies already assigned to first conformer: 11367 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CU': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' CU': 4, ' NA': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' CU': 4, ' NA': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Unusual residues: {' CU': 4} Inner-chain residues flagged as termini: ['pdbres="TRP D 801 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 29 Unusual residues: {' CU': 4, ' NA': 1} Inner-chain residues flagged as termini: ['pdbres="TRP E 801 "'] Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Unusual residues: {' CU': 4} Inner-chain residues flagged as termini: ['pdbres="TRP F 801 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Chain: "A" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 525 Classifications: {'water': 525} Link IDs: {None: 524} Chain: "B" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 520 Classifications: {'water': 520} Link IDs: {None: 519} Chain: "C" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 540 Classifications: {'water': 540} Link IDs: {None: 539} Chain: "D" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 529 Classifications: {'water': 529} Link IDs: {None: 528} Chain: "E" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 523 Classifications: {'water': 523} Link IDs: {None: 522} Chain: "F" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 533 Classifications: {'water': 533} Link IDs: {None: 532} Time building chain proxies: 41.89, per 1000 atoms: 0.59 Number of scatterers: 71225 At special positions: 0 Unit cell: (137.896, 134.632, 113.417, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cu 24 28.99 S 396 16.00 Na 3 11.00 O 9278 8.00 N 5754 7.00 C 21840 6.00 H 33930 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 544 " distance=2.03 Simple disulfide: pdb=" SG CYS A 663 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 293 " - pdb=" SG CYS B 544 " distance=2.03 Simple disulfide: pdb=" SG CYS B 663 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 293 " - pdb=" SG CYS C 544 " distance=2.03 Simple disulfide: pdb=" SG CYS C 663 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS D 293 " - pdb=" SG CYS D 544 " distance=2.03 Simple disulfide: pdb=" SG CYS D 663 " - pdb=" SG CYS D 668 " distance=2.03 Simple disulfide: pdb=" SG CYS E 293 " - pdb=" SG CYS E 544 " distance=2.03 Simple disulfide: pdb=" SG CYS E 663 " - pdb=" SG CYS E 668 " distance=2.03 Simple disulfide: pdb=" SG CYS F 293 " - pdb=" SG CYS F 544 " distance=2.03 Simple disulfide: pdb=" SG CYS F 663 " - pdb=" SG CYS F 668 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 45.61 Conformation dependent library (CDL) restraints added in 9.7 seconds 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7884 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 36 sheets defined 44.9% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.25 Creating SS restraints... Processing helix chain 'A' and resid 40 through 52 Processing helix chain 'A' and resid 76 through 80 Processing helix chain 'A' and resid 82 through 96 removed outlier: 3.777A pdb=" N VAL A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 124 Processing helix chain 'A' and resid 127 through 140 removed outlier: 3.875A pdb=" N GLU A 140 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 158 Processing helix chain 'A' and resid 159 through 162 removed outlier: 3.788A pdb=" N SER A 162 " --> pdb=" O SER A 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 159 through 162' Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 174 through 177 Processing helix chain 'A' and resid 179 through 193 Processing helix chain 'A' and resid 197 through 205 Processing helix chain 'A' and resid 227 through 231 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 238 through 252 Processing helix chain 'A' and resid 261 through 266 Processing helix chain 'A' and resid 267 through 290 removed outlier: 3.542A pdb=" N HIS A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 355 Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'A' and resid 372 through 382 Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 420 through 424 removed outlier: 3.544A pdb=" N MET A 424 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 430 Processing helix chain 'A' and resid 431 through 452 removed outlier: 3.563A pdb=" N TRP A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU A 443 " --> pdb=" O LYS A 439 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N TYR A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 461 Processing helix chain 'A' and resid 487 through 490 Processing helix chain 'A' and resid 493 through 500 Processing helix chain 'A' and resid 550 through 555 Processing helix chain 'A' and resid 556 through 558 No H-bonds generated for 'chain 'A' and resid 556 through 558' Processing helix chain 'A' and resid 580 through 582 No H-bonds generated for 'chain 'A' and resid 580 through 582' Processing helix chain 'A' and resid 609 through 617 removed outlier: 4.172A pdb=" N ARG A 615 " --> pdb=" O TRP A 611 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 616 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 661 removed outlier: 3.867A pdb=" N ALA A 657 " --> pdb=" O ASP A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 709 removed outlier: 3.784A pdb=" N ASN A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 704 through 709' Processing helix chain 'A' and resid 726 through 731 removed outlier: 3.824A pdb=" N LYS A 730 " --> pdb=" O TYR A 727 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASP A 731 " --> pdb=" O LEU A 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 52 Processing helix chain 'B' and resid 76 through 80 Processing helix chain 'B' and resid 82 through 96 removed outlier: 3.777A pdb=" N VAL B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 124 Processing helix chain 'B' and resid 127 through 140 removed outlier: 3.876A pdb=" N GLU B 140 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 158 Processing helix chain 'B' and resid 159 through 162 removed outlier: 3.788A pdb=" N SER B 162 " --> pdb=" O SER B 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 159 through 162' Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 179 through 193 Processing helix chain 'B' and resid 197 through 205 Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 238 through 252 Processing helix chain 'B' and resid 261 through 266 Processing helix chain 'B' and resid 267 through 290 removed outlier: 3.541A pdb=" N HIS B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 355 Processing helix chain 'B' and resid 369 through 371 No H-bonds generated for 'chain 'B' and resid 369 through 371' Processing helix chain 'B' and resid 372 through 382 Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 420 through 424 removed outlier: 3.544A pdb=" N MET B 424 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 430 Processing helix chain 'B' and resid 431 through 452 removed outlier: 3.563A pdb=" N TRP B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU B 443 " --> pdb=" O LYS B 439 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N TYR B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE B 445 " --> pdb=" O ILE B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 461 Processing helix chain 'B' and resid 487 through 490 Processing helix chain 'B' and resid 493 through 500 Processing helix chain 'B' and resid 550 through 555 Processing helix chain 'B' and resid 556 through 558 No H-bonds generated for 'chain 'B' and resid 556 through 558' Processing helix chain 'B' and resid 580 through 582 No H-bonds generated for 'chain 'B' and resid 580 through 582' Processing helix chain 'B' and resid 609 through 617 removed outlier: 4.172A pdb=" N ARG B 615 " --> pdb=" O TRP B 611 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE B 616 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.867A pdb=" N ALA B 657 " --> pdb=" O ASP B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 709 removed outlier: 3.785A pdb=" N ASN B 708 " --> pdb=" O LEU B 704 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET B 709 " --> pdb=" O ALA B 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 704 through 709' Processing helix chain 'B' and resid 726 through 731 removed outlier: 3.824A pdb=" N LYS B 730 " --> pdb=" O TYR B 727 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASP B 731 " --> pdb=" O LEU B 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 52 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 82 through 96 removed outlier: 3.777A pdb=" N VAL C 86 " --> pdb=" O LYS C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 124 Processing helix chain 'C' and resid 127 through 140 removed outlier: 3.875A pdb=" N GLU C 140 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 158 Processing helix chain 'C' and resid 159 through 162 removed outlier: 3.788A pdb=" N SER C 162 " --> pdb=" O SER C 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 159 through 162' Processing helix chain 'C' and resid 168 through 173 Processing helix chain 'C' and resid 174 through 177 Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 197 through 205 Processing helix chain 'C' and resid 227 through 231 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 238 through 252 Processing helix chain 'C' and resid 261 through 266 Processing helix chain 'C' and resid 267 through 290 removed outlier: 3.541A pdb=" N HIS C 290 " --> pdb=" O GLU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 355 Processing helix chain 'C' and resid 369 through 371 No H-bonds generated for 'chain 'C' and resid 369 through 371' Processing helix chain 'C' and resid 372 through 382 Processing helix chain 'C' and resid 400 through 405 Processing helix chain 'C' and resid 420 through 424 removed outlier: 3.543A pdb=" N MET C 424 " --> pdb=" O ALA C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 430 Processing helix chain 'C' and resid 431 through 452 removed outlier: 3.563A pdb=" N TRP C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU C 443 " --> pdb=" O LYS C 439 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N TYR C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE C 445 " --> pdb=" O ILE C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 461 Processing helix chain 'C' and resid 487 through 490 Processing helix chain 'C' and resid 493 through 500 Processing helix chain 'C' and resid 550 through 555 Processing helix chain 'C' and resid 556 through 558 No H-bonds generated for 'chain 'C' and resid 556 through 558' Processing helix chain 'C' and resid 580 through 582 No H-bonds generated for 'chain 'C' and resid 580 through 582' Processing helix chain 'C' and resid 609 through 617 removed outlier: 4.173A pdb=" N ARG C 615 " --> pdb=" O TRP C 611 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE C 616 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 661 removed outlier: 3.867A pdb=" N ALA C 657 " --> pdb=" O ASP C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 709 removed outlier: 3.785A pdb=" N ASN C 708 " --> pdb=" O LEU C 704 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET C 709 " --> pdb=" O ALA C 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 704 through 709' Processing helix chain 'C' and resid 726 through 731 removed outlier: 3.825A pdb=" N LYS C 730 " --> pdb=" O TYR C 727 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASP C 731 " --> pdb=" O LEU C 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 52 Processing helix chain 'D' and resid 76 through 80 Processing helix chain 'D' and resid 82 through 96 removed outlier: 3.778A pdb=" N VAL D 86 " --> pdb=" O LYS D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 124 Processing helix chain 'D' and resid 127 through 140 removed outlier: 3.876A pdb=" N GLU D 140 " --> pdb=" O CYS D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 158 Processing helix chain 'D' and resid 159 through 162 removed outlier: 3.787A pdb=" N SER D 162 " --> pdb=" O SER D 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 159 through 162' Processing helix chain 'D' and resid 168 through 173 Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 179 through 193 Processing helix chain 'D' and resid 197 through 205 Processing helix chain 'D' and resid 227 through 231 Processing helix chain 'D' and resid 232 through 237 Processing helix chain 'D' and resid 238 through 252 Processing helix chain 'D' and resid 261 through 266 Processing helix chain 'D' and resid 267 through 290 removed outlier: 3.542A pdb=" N HIS D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 355 Processing helix chain 'D' and resid 369 through 371 No H-bonds generated for 'chain 'D' and resid 369 through 371' Processing helix chain 'D' and resid 372 through 382 Processing helix chain 'D' and resid 400 through 405 Processing helix chain 'D' and resid 420 through 424 removed outlier: 3.544A pdb=" N MET D 424 " --> pdb=" O ALA D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 430 Processing helix chain 'D' and resid 431 through 452 removed outlier: 3.563A pdb=" N TRP D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU D 443 " --> pdb=" O LYS D 439 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TYR D 444 " --> pdb=" O LEU D 440 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE D 445 " --> pdb=" O ILE D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 461 Processing helix chain 'D' and resid 487 through 490 Processing helix chain 'D' and resid 493 through 500 Processing helix chain 'D' and resid 550 through 555 Processing helix chain 'D' and resid 556 through 558 No H-bonds generated for 'chain 'D' and resid 556 through 558' Processing helix chain 'D' and resid 580 through 582 No H-bonds generated for 'chain 'D' and resid 580 through 582' Processing helix chain 'D' and resid 609 through 617 removed outlier: 4.172A pdb=" N ARG D 615 " --> pdb=" O TRP D 611 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE D 616 " --> pdb=" O TYR D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.867A pdb=" N ALA D 657 " --> pdb=" O ASP D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 704 through 709 removed outlier: 3.785A pdb=" N ASN D 708 " --> pdb=" O LEU D 704 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET D 709 " --> pdb=" O ALA D 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 704 through 709' Processing helix chain 'D' and resid 726 through 731 removed outlier: 3.824A pdb=" N LYS D 730 " --> pdb=" O TYR D 727 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ASP D 731 " --> pdb=" O LEU D 728 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 52 Processing helix chain 'E' and resid 76 through 80 Processing helix chain 'E' and resid 82 through 96 removed outlier: 3.777A pdb=" N VAL E 86 " --> pdb=" O LYS E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 124 Processing helix chain 'E' and resid 127 through 140 removed outlier: 3.875A pdb=" N GLU E 140 " --> pdb=" O CYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 158 Processing helix chain 'E' and resid 159 through 162 removed outlier: 3.788A pdb=" N SER E 162 " --> pdb=" O SER E 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 159 through 162' Processing helix chain 'E' and resid 168 through 173 Processing helix chain 'E' and resid 174 through 177 Processing helix chain 'E' and resid 179 through 193 Processing helix chain 'E' and resid 197 through 205 Processing helix chain 'E' and resid 227 through 231 Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 238 through 252 Processing helix chain 'E' and resid 261 through 266 Processing helix chain 'E' and resid 267 through 290 removed outlier: 3.542A pdb=" N HIS E 290 " --> pdb=" O GLU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 355 Processing helix chain 'E' and resid 369 through 371 No H-bonds generated for 'chain 'E' and resid 369 through 371' Processing helix chain 'E' and resid 372 through 382 Processing helix chain 'E' and resid 400 through 405 Processing helix chain 'E' and resid 420 through 424 removed outlier: 3.543A pdb=" N MET E 424 " --> pdb=" O ALA E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 430 Processing helix chain 'E' and resid 431 through 452 removed outlier: 3.564A pdb=" N TRP E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU E 443 " --> pdb=" O LYS E 439 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TYR E 444 " --> pdb=" O LEU E 440 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE E 445 " --> pdb=" O ILE E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 461 Processing helix chain 'E' and resid 487 through 490 Processing helix chain 'E' and resid 493 through 500 Processing helix chain 'E' and resid 550 through 555 Processing helix chain 'E' and resid 556 through 558 No H-bonds generated for 'chain 'E' and resid 556 through 558' Processing helix chain 'E' and resid 580 through 582 No H-bonds generated for 'chain 'E' and resid 580 through 582' Processing helix chain 'E' and resid 609 through 617 removed outlier: 4.172A pdb=" N ARG E 615 " --> pdb=" O TRP E 611 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE E 616 " --> pdb=" O TYR E 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 653 through 661 removed outlier: 3.866A pdb=" N ALA E 657 " --> pdb=" O ASP E 653 " (cutoff:3.500A) Processing helix chain 'E' and resid 704 through 709 removed outlier: 3.784A pdb=" N ASN E 708 " --> pdb=" O LEU E 704 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET E 709 " --> pdb=" O ALA E 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 704 through 709' Processing helix chain 'E' and resid 726 through 731 removed outlier: 3.824A pdb=" N LYS E 730 " --> pdb=" O TYR E 727 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ASP E 731 " --> pdb=" O LEU E 728 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 52 Processing helix chain 'F' and resid 76 through 80 Processing helix chain 'F' and resid 82 through 96 removed outlier: 3.777A pdb=" N VAL F 86 " --> pdb=" O LYS F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 124 Processing helix chain 'F' and resid 127 through 140 removed outlier: 3.875A pdb=" N GLU F 140 " --> pdb=" O CYS F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 158 Processing helix chain 'F' and resid 159 through 162 removed outlier: 3.787A pdb=" N SER F 162 " --> pdb=" O SER F 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 159 through 162' Processing helix chain 'F' and resid 168 through 173 Processing helix chain 'F' and resid 174 through 177 Processing helix chain 'F' and resid 179 through 193 Processing helix chain 'F' and resid 197 through 205 Processing helix chain 'F' and resid 227 through 231 Processing helix chain 'F' and resid 232 through 237 Processing helix chain 'F' and resid 238 through 252 Processing helix chain 'F' and resid 261 through 266 Processing helix chain 'F' and resid 267 through 290 removed outlier: 3.542A pdb=" N HIS F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 355 Processing helix chain 'F' and resid 369 through 371 No H-bonds generated for 'chain 'F' and resid 369 through 371' Processing helix chain 'F' and resid 372 through 382 Processing helix chain 'F' and resid 400 through 405 Processing helix chain 'F' and resid 420 through 424 removed outlier: 3.543A pdb=" N MET F 424 " --> pdb=" O ALA F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 430 Processing helix chain 'F' and resid 431 through 452 removed outlier: 3.563A pdb=" N TRP F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU F 443 " --> pdb=" O LYS F 439 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N TYR F 444 " --> pdb=" O LEU F 440 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE F 445 " --> pdb=" O ILE F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 461 Processing helix chain 'F' and resid 487 through 490 Processing helix chain 'F' and resid 493 through 500 Processing helix chain 'F' and resid 550 through 555 Processing helix chain 'F' and resid 556 through 558 No H-bonds generated for 'chain 'F' and resid 556 through 558' Processing helix chain 'F' and resid 580 through 582 No H-bonds generated for 'chain 'F' and resid 580 through 582' Processing helix chain 'F' and resid 609 through 617 removed outlier: 4.172A pdb=" N ARG F 615 " --> pdb=" O TRP F 611 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE F 616 " --> pdb=" O TYR F 612 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 661 removed outlier: 3.867A pdb=" N ALA F 657 " --> pdb=" O ASP F 653 " (cutoff:3.500A) Processing helix chain 'F' and resid 704 through 709 removed outlier: 3.784A pdb=" N ASN F 708 " --> pdb=" O LEU F 704 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET F 709 " --> pdb=" O ALA F 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 704 through 709' Processing helix chain 'F' and resid 726 through 731 removed outlier: 3.824A pdb=" N LYS F 730 " --> pdb=" O TYR F 727 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASP F 731 " --> pdb=" O LEU F 728 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 209 removed outlier: 3.817A pdb=" N HIS A 511 " --> pdb=" O TRP A 218 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU A 475 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL A 530 " --> pdb=" O LYS A 567 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LYS A 567 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N CYS A 532 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU A 565 " --> pdb=" O CYS A 532 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 534 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER A 563 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 536 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 303 through 304 Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AA4, first strand: chain 'A' and resid 465 through 472 removed outlier: 6.575A pdb=" N ASP A 523 " --> pdb=" O GLU A 468 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL A 470 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR A 521 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR A 472 " --> pdb=" O LYS A 519 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS A 519 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 585 through 586 Processing sheet with id=AA6, first strand: chain 'A' and resid 719 through 720 Processing sheet with id=AA7, first strand: chain 'B' and resid 206 through 209 removed outlier: 3.817A pdb=" N HIS B 511 " --> pdb=" O TRP B 218 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU B 475 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL B 530 " --> pdb=" O LYS B 567 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS B 567 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N CYS B 532 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU B 565 " --> pdb=" O CYS B 532 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 534 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER B 563 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B 536 " --> pdb=" O ILE B 561 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 303 through 304 Processing sheet with id=AA9, first strand: chain 'B' and resid 356 through 358 Processing sheet with id=AB1, first strand: chain 'B' and resid 465 through 472 removed outlier: 6.576A pdb=" N ASP B 523 " --> pdb=" O GLU B 468 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL B 470 " --> pdb=" O THR B 521 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR B 521 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR B 472 " --> pdb=" O LYS B 519 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS B 519 " --> pdb=" O THR B 472 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 585 through 586 Processing sheet with id=AB3, first strand: chain 'B' and resid 719 through 720 Processing sheet with id=AB4, first strand: chain 'C' and resid 206 through 209 removed outlier: 3.816A pdb=" N HIS C 511 " --> pdb=" O TRP C 218 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU C 475 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL C 530 " --> pdb=" O LYS C 567 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS C 567 " --> pdb=" O VAL C 530 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N CYS C 532 " --> pdb=" O LEU C 565 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU C 565 " --> pdb=" O CYS C 532 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL C 534 " --> pdb=" O SER C 563 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER C 563 " --> pdb=" O VAL C 534 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL C 536 " --> pdb=" O ILE C 561 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 303 through 304 Processing sheet with id=AB6, first strand: chain 'C' and resid 356 through 358 Processing sheet with id=AB7, first strand: chain 'C' and resid 465 through 472 removed outlier: 6.576A pdb=" N ASP C 523 " --> pdb=" O GLU C 468 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL C 470 " --> pdb=" O THR C 521 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR C 521 " --> pdb=" O VAL C 470 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR C 472 " --> pdb=" O LYS C 519 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS C 519 " --> pdb=" O THR C 472 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 585 through 586 Processing sheet with id=AB9, first strand: chain 'C' and resid 719 through 720 Processing sheet with id=AC1, first strand: chain 'D' and resid 206 through 209 removed outlier: 3.817A pdb=" N HIS D 511 " --> pdb=" O TRP D 218 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU D 475 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL D 530 " --> pdb=" O LYS D 567 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LYS D 567 " --> pdb=" O VAL D 530 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N CYS D 532 " --> pdb=" O LEU D 565 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU D 565 " --> pdb=" O CYS D 532 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL D 534 " --> pdb=" O SER D 563 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER D 563 " --> pdb=" O VAL D 534 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL D 536 " --> pdb=" O ILE D 561 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 303 through 304 Processing sheet with id=AC3, first strand: chain 'D' and resid 356 through 358 Processing sheet with id=AC4, first strand: chain 'D' and resid 465 through 472 removed outlier: 6.576A pdb=" N ASP D 523 " --> pdb=" O GLU D 468 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL D 470 " --> pdb=" O THR D 521 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR D 521 " --> pdb=" O VAL D 470 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR D 472 " --> pdb=" O LYS D 519 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS D 519 " --> pdb=" O THR D 472 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 585 through 586 Processing sheet with id=AC6, first strand: chain 'D' and resid 719 through 720 Processing sheet with id=AC7, first strand: chain 'E' and resid 206 through 209 removed outlier: 3.817A pdb=" N HIS E 511 " --> pdb=" O TRP E 218 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU E 475 " --> pdb=" O TYR E 700 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL E 530 " --> pdb=" O LYS E 567 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS E 567 " --> pdb=" O VAL E 530 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N CYS E 532 " --> pdb=" O LEU E 565 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU E 565 " --> pdb=" O CYS E 532 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL E 534 " --> pdb=" O SER E 563 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER E 563 " --> pdb=" O VAL E 534 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL E 536 " --> pdb=" O ILE E 561 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 303 through 304 Processing sheet with id=AC9, first strand: chain 'E' and resid 356 through 358 Processing sheet with id=AD1, first strand: chain 'E' and resid 465 through 472 removed outlier: 6.575A pdb=" N ASP E 523 " --> pdb=" O GLU E 468 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL E 470 " --> pdb=" O THR E 521 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR E 521 " --> pdb=" O VAL E 470 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR E 472 " --> pdb=" O LYS E 519 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS E 519 " --> pdb=" O THR E 472 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 585 through 586 Processing sheet with id=AD3, first strand: chain 'E' and resid 719 through 720 Processing sheet with id=AD4, first strand: chain 'F' and resid 206 through 209 removed outlier: 3.817A pdb=" N HIS F 511 " --> pdb=" O TRP F 218 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU F 475 " --> pdb=" O TYR F 700 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL F 530 " --> pdb=" O LYS F 567 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS F 567 " --> pdb=" O VAL F 530 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N CYS F 532 " --> pdb=" O LEU F 565 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU F 565 " --> pdb=" O CYS F 532 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL F 534 " --> pdb=" O SER F 563 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER F 563 " --> pdb=" O VAL F 534 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL F 536 " --> pdb=" O ILE F 561 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 303 through 304 Processing sheet with id=AD6, first strand: chain 'F' and resid 356 through 358 Processing sheet with id=AD7, first strand: chain 'F' and resid 465 through 472 removed outlier: 6.576A pdb=" N ASP F 523 " --> pdb=" O GLU F 468 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL F 470 " --> pdb=" O THR F 521 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR F 521 " --> pdb=" O VAL F 470 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR F 472 " --> pdb=" O LYS F 519 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS F 519 " --> pdb=" O THR F 472 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 585 through 586 Processing sheet with id=AD9, first strand: chain 'F' and resid 719 through 720 1356 hydrogen bonds defined for protein. 3684 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: 27.90 Time building geometry restraints manager: 48.11 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: 33900 1.03 - 1.23: 30 1.23 - 1.42: 14640 1.42 - 1.62: 19548 1.62 - 1.81: 738 Bond restraints: 68856 Sorted by residual: bond pdb=" CA MET A 97 " pdb=" C MET A 97 " ideal model delta sigma weight residual 1.523 1.531 -0.007 1.34e-02 5.57e+03 3.07e-01 bond pdb=" CA MET C 97 " pdb=" C MET C 97 " ideal model delta sigma weight residual 1.523 1.531 -0.007 1.34e-02 5.57e+03 2.97e-01 bond pdb=" C LYS C 110 " pdb=" O LYS C 110 " ideal model delta sigma weight residual 1.236 1.242 -0.006 1.15e-02 7.56e+03 2.46e-01 bond pdb=" C MET E 272 " pdb=" O MET E 272 " ideal model delta sigma weight residual 1.236 1.242 -0.006 1.15e-02 7.56e+03 2.41e-01 bond pdb=" C LYS F 110 " pdb=" O LYS F 110 " ideal model delta sigma weight residual 1.236 1.242 -0.006 1.15e-02 7.56e+03 2.39e-01 ... (remaining 68851 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.15: 1401 107.15 - 113.86: 82354 113.86 - 120.58: 22342 120.58 - 127.29: 17923 127.29 - 134.01: 450 Bond angle restraints: 124470 Sorted by residual: angle pdb=" C ILE F 616 " pdb=" CA ILE F 616 " pdb=" CB ILE F 616 " ideal model delta sigma weight residual 112.36 110.47 1.89 1.37e+00 5.33e-01 1.89e+00 angle pdb=" C ILE B 616 " pdb=" CA ILE B 616 " pdb=" CB ILE B 616 " ideal model delta sigma weight residual 112.36 110.48 1.88 1.37e+00 5.33e-01 1.89e+00 angle pdb=" C LYS E 209 " pdb=" N ASP E 210 " pdb=" CA ASP E 210 " ideal model delta sigma weight residual 123.05 125.21 -2.16 1.57e+00 4.06e-01 1.89e+00 angle pdb=" C LYS D 209 " pdb=" N ASP D 210 " pdb=" CA ASP D 210 " ideal model delta sigma weight residual 123.05 125.20 -2.15 1.57e+00 4.06e-01 1.87e+00 angle pdb=" C ILE D 616 " pdb=" CA ILE D 616 " pdb=" CB ILE D 616 " ideal model delta sigma weight residual 112.36 110.49 1.87 1.37e+00 5.33e-01 1.86e+00 ... (remaining 124465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.61: 30797 15.61 - 31.23: 1069 31.23 - 46.84: 342 46.84 - 62.45: 120 62.45 - 78.06: 18 Dihedral angle restraints: 32346 sinusoidal: 17520 harmonic: 14826 Sorted by residual: dihedral pdb=" N MET F 46 " pdb=" CA MET F 46 " pdb=" CB MET F 46 " pdb=" CG MET F 46 " ideal model delta sinusoidal sigma weight residual -180.00 -131.44 -48.56 3 1.50e+01 4.44e-03 8.66e+00 dihedral pdb=" N MET B 46 " pdb=" CA MET B 46 " pdb=" CB MET B 46 " pdb=" CG MET B 46 " ideal model delta sinusoidal sigma weight residual -180.00 -131.45 -48.55 3 1.50e+01 4.44e-03 8.65e+00 dihedral pdb=" N MET D 46 " pdb=" CA MET D 46 " pdb=" CB MET D 46 " pdb=" CG MET D 46 " ideal model delta sinusoidal sigma weight residual -180.00 -131.48 -48.52 3 1.50e+01 4.44e-03 8.65e+00 ... (remaining 32343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3345 0.029 - 0.058: 1108 0.058 - 0.087: 206 0.087 - 0.116: 244 0.116 - 0.146: 65 Chirality restraints: 4968 Sorted by residual: chirality pdb=" CA ILE B 418 " pdb=" N ILE B 418 " pdb=" C ILE B 418 " pdb=" CB ILE B 418 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA ILE C 418 " pdb=" N ILE C 418 " pdb=" C ILE C 418 " pdb=" CB ILE C 418 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ILE A 418 " pdb=" N ILE A 418 " pdb=" C ILE A 418 " pdb=" CB ILE A 418 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 4965 not shown) Planarity restraints: 9840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE E 676 " -0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO E 677 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO E 677 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 677 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 676 " 0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO C 677 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO C 677 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 677 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 676 " -0.018 5.00e-02 4.00e+02 2.72e-02 1.19e+00 pdb=" N PRO D 677 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO D 677 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 677 " -0.014 5.00e-02 4.00e+02 ... (remaining 9837 not shown) Histogram of nonbonded interaction distances: 1.31 - 1.97: 362 1.97 - 2.63: 84664 2.63 - 3.29: 220576 3.29 - 3.94: 293239 3.94 - 4.60: 461306 Nonbonded interactions: 1060147 Sorted by model distance: nonbonded pdb="HD22 ASN F 573 " pdb=" O HOH F 903 " model vdw 1.315 1.850 nonbonded pdb="HD22 ASN C 573 " pdb=" O HOH C 903 " model vdw 1.332 1.850 nonbonded pdb=" H THR B 420 " pdb=" OD2 ASP B 423 " model vdw 1.626 1.850 nonbonded pdb=" H THR C 420 " pdb=" OD2 ASP C 423 " model vdw 1.626 1.850 nonbonded pdb=" H THR F 420 " pdb=" OD2 ASP F 423 " model vdw 1.626 1.850 ... (remaining 1060142 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 34 through 102 or resid 104 through 111 or resid 113 throu \ gh 639 or resid 641 through 739 or resid 803 through 804)) selection = (chain 'B' and (resid 34 through 102 or resid 104 through 111 or resid 113 throu \ gh 639 or resid 641 through 739 or resid 803 through 804)) selection = (chain 'C' and (resid 34 through 102 or resid 104 through 111 or resid 113 throu \ gh 639 or resid 641 through 739 or resid 803 through 804)) selection = (chain 'D' and (resid 34 through 102 or resid 104 through 111 or resid 113 throu \ gh 639 or resid 641 through 739 or resid 802 through 803)) selection = (chain 'E' and (resid 34 through 102 or resid 104 through 111 or resid 113 throu \ gh 639 or resid 641 through 739 or resid 803 through 804)) selection = (chain 'F' and (resid 34 through 102 or resid 104 through 111 or resid 113 throu \ gh 639 or resid 641 through 739 or resid 802 through 803)) } 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=0.23 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: 4.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.130 Extract box with map and model: 12.330 Check model and map are aligned: 0.390 Set scattering table: 0.490 Process input model: 199.100 Find NCS groups from input model: 3.110 Set up NCS constraints: 0.250 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:10.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 231.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 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 : 0.002 0.015 34926 Z= 0.099 Angle : 0.399 3.821 47022 Z= 0.219 Chirality : 0.038 0.146 4968 Planarity : 0.003 0.028 5904 Dihedral : 9.004 78.063 13386 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.16 % Allowed : 1.43 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.63 (0.14), residues: 4068 helix: 1.26 (0.14), residues: 1446 sheet: 0.38 (0.21), residues: 606 loop : 1.44 (0.15), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 273 HIS 0.003 0.001 HIS D 54 PHE 0.011 0.001 PHE D 537 TYR 0.011 0.001 TYR F 149 ARG 0.002 0.000 ARG A 398 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 3738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 828 time to evaluate : 4.336 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: A 36 MET cc_start: 0.1390 (ttt) cc_final: 0.1149 (ttp) REVERT: A 78 ASP cc_start: 0.6046 (p0) cc_final: 0.5728 (p0) REVERT: B 36 MET cc_start: 0.1134 (ttt) cc_final: 0.0926 (ttp) REVERT: B 50 LYS cc_start: 0.7853 (mttt) cc_final: 0.7637 (mtmt) REVERT: B 72 VAL cc_start: 0.6258 (t) cc_final: 0.5968 (m) REVERT: B 226 MET cc_start: 0.8782 (mmm) cc_final: 0.8535 (mmm) REVERT: B 292 MET cc_start: 0.8549 (mtm) cc_final: 0.8344 (mtp) REVERT: B 732 MET cc_start: 0.7944 (mmp) cc_final: 0.7723 (mmp) REVERT: C 36 MET cc_start: 0.1530 (ttt) cc_final: 0.1251 (ttp) REVERT: C 129 ASP cc_start: 0.6769 (t70) cc_final: 0.6548 (t0) REVERT: C 213 MET cc_start: 0.7758 (ttm) cc_final: 0.7367 (ttp) REVERT: C 320 MET cc_start: 0.9072 (mtt) cc_final: 0.8862 (mtt) REVERT: C 363 THR cc_start: 0.7861 (p) cc_final: 0.7571 (m) REVERT: C 732 MET cc_start: 0.7991 (mmp) cc_final: 0.7755 (mmp) REVERT: D 36 MET cc_start: 0.1374 (ttt) cc_final: 0.1135 (ttp) REVERT: D 78 ASP cc_start: 0.6048 (p0) cc_final: 0.5719 (p0) REVERT: E 36 MET cc_start: 0.1241 (ttt) cc_final: 0.1026 (ttp) REVERT: E 50 LYS cc_start: 0.7860 (mttt) cc_final: 0.7653 (mtmt) REVERT: E 226 MET cc_start: 0.8796 (mmm) cc_final: 0.8526 (mmm) REVERT: E 292 MET cc_start: 0.8560 (mtm) cc_final: 0.8344 (mtp) REVERT: F 36 MET cc_start: 0.1527 (ttt) cc_final: 0.1243 (ttp) REVERT: F 129 ASP cc_start: 0.6755 (t70) cc_final: 0.6532 (t0) REVERT: F 213 MET cc_start: 0.7766 (ttm) cc_final: 0.7382 (ttp) REVERT: F 363 THR cc_start: 0.7863 (p) cc_final: 0.7572 (m) REVERT: F 732 MET cc_start: 0.7996 (mmp) cc_final: 0.7765 (mmp) outliers start: 6 outliers final: 0 residues processed: 828 average time/residue: 2.9427 time to fit residues: 2911.2452 Evaluate side-chains 662 residues out of total 3738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 662 time to evaluate : 4.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.6929 > 50: distance: 165 - 479: 21.321 distance: 168 - 476: 3.058 distance: 198 - 443: 34.130 distance: 201 - 440: 15.979 distance: 231 - 409: 31.746 distance: 234 - 406: 8.444 distance: 342 - 347: 28.632 distance: 347 - 348: 38.134 distance: 347 - 351: 14.779 distance: 348 - 349: 16.713 distance: 348 - 352: 52.396 distance: 348 - 353: 43.420 distance: 349 - 350: 15.990 distance: 349 - 354: 29.689 distance: 354 - 355: 8.886 distance: 354 - 362: 30.109 distance: 354 - 691: 17.356 distance: 355 - 356: 28.766 distance: 355 - 358: 28.105 distance: 355 - 363: 8.764 distance: 356 - 357: 33.980 distance: 356 - 371: 21.073 distance: 357 - 688: 19.418 distance: 358 - 359: 26.048 distance: 358 - 364: 16.148 distance: 358 - 365: 30.407 distance: 359 - 360: 12.744 distance: 359 - 366: 5.518 distance: 359 - 367: 6.771 distance: 360 - 361: 9.860 distance: 371 - 372: 21.766 distance: 371 - 377: 33.221 distance: 372 - 373: 16.673 distance: 372 - 375: 25.877 distance: 372 - 378: 26.467 distance: 373 - 374: 32.261 distance: 373 - 385: 10.025 distance: 375 - 376: 21.781 distance: 375 - 379: 21.479 distance: 375 - 380: 12.961 distance: 376 - 377: 18.957 distance: 376 - 381: 19.419 distance: 376 - 382: 17.447 distance: 377 - 383: 15.635 distance: 377 - 384: 21.086 distance: 385 - 386: 10.927 distance: 385 - 397: 21.272 distance: 385 - 658: 8.906 distance: 386 - 387: 33.518 distance: 386 - 389: 23.937 distance: 386 - 398: 17.486 distance: 387 - 388: 6.260 distance: 387 - 406: 26.619 distance: 388 - 655: 23.555 distance: 389 - 390: 10.382 distance: 389 - 399: 20.442 distance: 389 - 400: 9.061 distance: 390 - 391: 7.300 distance: 390 - 392: 25.987 distance: 391 - 393: 19.160 distance: 391 - 401: 14.637 distance: 392 - 394: 11.808 distance: 392 - 402: 32.229 distance: 393 - 395: 5.011 distance: 393 - 403: 5.939 distance: 394 - 395: 10.932 distance: 394 - 404: 6.105 distance: 395 - 396: 17.158 distance: 396 - 405: 20.951 distance: 406 - 407: 14.210 distance: 406 - 415: 28.143 distance: 407 - 408: 17.998 distance: 407 - 410: 26.239 distance: 407 - 416: 31.105 distance: 408 - 409: 22.789 distance: 408 - 423: 28.443 distance: 410 - 411: 18.327 distance: 410 - 417: 29.379 distance: 410 - 418: 38.175 distance: 411 - 412: 13.280 distance: 411 - 419: 19.985 distance: 411 - 420: 21.547 distance: 412 - 413: 6.157 distance: 412 - 414: 5.197 distance: 414 - 421: 4.666 distance: 414 - 422: 8.406 distance: 423 - 424: 14.219 distance: 423 - 431: 24.672 distance: 423 - 636: 15.624 distance: 424 - 425: 7.131 distance: 424 - 427: 21.146 distance: 424 - 432: 35.453 distance: 425 - 426: 30.902 distance: 425 - 440: 9.320 distance: 426 - 633: 17.266 distance: 427 - 428: 36.646 distance: 427 - 433: 37.606 distance: 427 - 434: 42.304 distance: 428 - 429: 5.771 distance: 428 - 435: 5.370 distance: 428 - 436: 15.511 distance: 429 - 430: 8.762 distance: 430 - 437: 4.765 distance: 440 - 441: 10.319 distance: 440 - 451: 39.412 distance: 441 - 442: 11.714 distance: 441 - 444: 17.731 distance: 441 - 452: 19.031 distance: 442 - 443: 31.003 distance: 442 - 460: 35.535 distance: 444 - 445: 5.955 distance: 444 - 453: 13.305 distance: 444 - 454: 11.591 distance: 445 - 446: 7.615 distance: 445 - 447: 8.102 distance: 446 - 448: 4.503 distance: 446 - 455: 6.366 distance: 447 - 449: 4.460 distance: 447 - 456: 6.123 distance: 450 - 459: 3.180 distance: 460 - 461: 23.580 distance: 460 - 467: 25.728 distance: 460 - 604: 32.433 distance: 461 - 462: 35.613 distance: 461 - 464: 5.141 distance: 461 - 468: 12.527 distance: 462 - 463: 38.986 distance: 462 - 476: 25.827 distance: 463 - 601: 11.306 distance: 464 - 465: 7.856 distance: 464 - 466: 11.440 distance: 464 - 469: 14.009 distance: 465 - 470: 15.174 distance: 465 - 471: 13.317 distance: 465 - 472: 13.355 distance: 466 - 473: 15.902 distance: 466 - 474: 10.409 distance: 466 - 475: 13.547 distance: 476 - 477: 11.634 distance: 476 - 484: 15.513 distance: 477 - 478: 14.410 distance: 477 - 480: 8.398 distance: 477 - 485: 25.490 distance: 478 - 479: 15.730 distance: 478 - 495: 34.550 distance: 480 - 481: 9.293 distance: 480 - 482: 13.857 distance: 480 - 486: 11.428 distance: 481 - 487: 5.349 distance: 481 - 488: 3.196 distance: 482 - 489: 10.494 distance: 482 - 490: 7.501 distance: 482 - 491: 6.535 distance: 483 - 492: 3.958 distance: 483 - 493: 4.443 distance: 483 - 494: 4.295 distance: 495 - 498: 11.768 distance: 495 - 502: 20.306 distance: 495 - 511: 20.959 distance: 495 - 515: 22.373 distance: 496 - 497: 40.246 distance: 496 - 498: 24.930 distance: 496 - 511: 34.658 distance: 496 - 524: 28.242 distance: 498 - 499: 6.113 distance: 498 - 503: 22.964 distance: 499 - 500: 6.391 distance: 499 - 501: 13.086 distance: 499 - 504: 15.331 distance: 500 - 505: 9.048 distance: 500 - 506: 9.820 distance: 500 - 507: 12.010 distance: 501 - 508: 4.020 distance: 501 - 510: 5.579 distance: 511 - 512: 18.505 distance: 511 - 516: 13.614 distance: 512 - 513: 7.164 distance: 512 - 514: 13.026 distance: 512 - 517: 6.910 distance: 513 - 518: 4.903 distance: 513 - 519: 3.979 distance: 513 - 520: 10.053 distance: 514 - 521: 15.453 distance: 514 - 522: 11.413 distance: 514 - 523: 10.360