Starting phenix.real_space_refine on Fri Aug 9 00:13:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ep0_28494/08_2024/8ep0_28494.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ep0_28494/08_2024/8ep0_28494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ep0_28494/08_2024/8ep0_28494.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ep0_28494/08_2024/8ep0_28494.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ep0_28494/08_2024/8ep0_28494.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ep0_28494/08_2024/8ep0_28494.cif" } resolution = 4.9 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= 0.004 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 15696 2.51 5 N 4108 2.21 5 O 4488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "B PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 377": "OE1" <-> "OE2" Residue "C PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 377": "OE1" <-> "OE2" Residue "D PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 377": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 24408 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5220 Classifications: {'peptide': 701} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 24, 'TRANS': 676} Chain breaks: 2 Unresolved non-hydrogen bonds: 457 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 371 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 11, 'GLU%COO:plan': 1, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 246 Chain: "B" Number of atoms: 5220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5220 Classifications: {'peptide': 701} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 24, 'TRANS': 676} Chain breaks: 2 Unresolved non-hydrogen bonds: 457 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 371 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 11, 'GLU%COO:plan': 1, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 246 Chain: "C" Number of atoms: 5220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5220 Classifications: {'peptide': 701} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 24, 'TRANS': 676} Chain breaks: 2 Unresolved non-hydrogen bonds: 457 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 371 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 11, 'GLU%COO:plan': 1, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 246 Chain: "D" Number of atoms: 5220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5220 Classifications: {'peptide': 701} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 24, 'TRANS': 676} Chain breaks: 2 Unresolved non-hydrogen bonds: 457 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 371 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 11, 'GLU%COO:plan': 1, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 246 Chain: "E" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 882 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 142 Chain: "F" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 882 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 142 Chain: "G" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 882 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 142 Chain: "H" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 882 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 142 Time building chain proxies: 13.48, per 1000 atoms: 0.55 Number of scatterers: 24408 At special positions: 0 Unit cell: (169.56, 169.56, 149.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 116 16.00 O 4488 8.00 N 4108 7.00 C 15696 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 - 3.50 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: 9.94 Conformation dependent library (CDL) restraints added in 4.9 seconds 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6400 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 20 sheets defined 65.4% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'A' and resid 16 through 26 removed outlier: 3.995A pdb=" N ASN A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 175 through 189 removed outlier: 3.845A pdb=" N LYS A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N HIS A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 removed outlier: 4.058A pdb=" N ASP A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 242 Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 248 through 269 Processing helix chain 'A' and resid 283 through 304 removed outlier: 3.602A pdb=" N ARG A 288 " --> pdb=" O PRO A 284 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N MET A 289 " --> pdb=" O LYS A 285 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 4.115A pdb=" N ASN A 310 " --> pdb=" O TYR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 329 removed outlier: 3.646A pdb=" N LEU A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 342 removed outlier: 4.095A pdb=" N ARG A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LYS A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 347 removed outlier: 4.565A pdb=" N TYR A 347 " --> pdb=" O HIS A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 379 removed outlier: 3.650A pdb=" N LEU A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N PHE A 379 " --> pdb=" O ASP A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 418 through 435 Processing helix chain 'A' and resid 446 through 473 removed outlier: 3.917A pdb=" N THR A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE A 468 " --> pdb=" O TYR A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 499 removed outlier: 4.875A pdb=" N ASN A 481 " --> pdb=" O GLN A 477 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR A 482 " --> pdb=" O MET A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 521 Processing helix chain 'A' and resid 524 through 532 Processing helix chain 'A' and resid 533 through 545 Processing helix chain 'A' and resid 545 through 552 Processing helix chain 'A' and resid 553 through 556 Processing helix chain 'A' and resid 559 through 570 Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 647 through 657 Processing helix chain 'A' and resid 657 through 668 removed outlier: 3.874A pdb=" N SER A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 696 Processing helix chain 'A' and resid 704 through 706 No H-bonds generated for 'chain 'A' and resid 704 through 706' Processing helix chain 'A' and resid 707 through 722 Processing helix chain 'B' and resid 16 through 26 removed outlier: 3.995A pdb=" N ASN B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 67 through 71 Processing helix chain 'B' and resid 76 through 90 Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 158 through 163 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 175 through 189 removed outlier: 3.845A pdb=" N LYS B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N HIS B 181 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 194 removed outlier: 4.059A pdb=" N ASP B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 242 Proline residue: B 236 - end of helix Processing helix chain 'B' and resid 248 through 269 Processing helix chain 'B' and resid 283 through 304 removed outlier: 3.602A pdb=" N ARG B 288 " --> pdb=" O PRO B 284 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N MET B 289 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE B 298 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 312 removed outlier: 4.114A pdb=" N ASN B 310 " --> pdb=" O TYR B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 329 removed outlier: 3.645A pdb=" N LEU B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 342 removed outlier: 4.095A pdb=" N ARG B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LYS B 340 " --> pdb=" O ARG B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 347 removed outlier: 4.565A pdb=" N TYR B 347 " --> pdb=" O HIS B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 379 removed outlier: 3.650A pdb=" N LEU B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N PHE B 379 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 418 through 435 Processing helix chain 'B' and resid 446 through 473 removed outlier: 3.917A pdb=" N THR B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE B 467 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE B 468 " --> pdb=" O TYR B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 499 removed outlier: 4.875A pdb=" N ASN B 481 " --> pdb=" O GLN B 477 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR B 482 " --> pdb=" O MET B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 521 Processing helix chain 'B' and resid 524 through 532 Processing helix chain 'B' and resid 533 through 545 Processing helix chain 'B' and resid 545 through 552 Processing helix chain 'B' and resid 553 through 556 Processing helix chain 'B' and resid 559 through 570 Processing helix chain 'B' and resid 620 through 625 Processing helix chain 'B' and resid 647 through 657 Processing helix chain 'B' and resid 657 through 668 removed outlier: 3.874A pdb=" N SER B 663 " --> pdb=" O ALA B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 696 Processing helix chain 'B' and resid 704 through 706 No H-bonds generated for 'chain 'B' and resid 704 through 706' Processing helix chain 'B' and resid 707 through 722 Processing helix chain 'C' and resid 16 through 26 removed outlier: 3.995A pdb=" N ASN C 26 " --> pdb=" O VAL C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 76 through 90 Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 168 through 172 Processing helix chain 'C' and resid 175 through 189 removed outlier: 3.845A pdb=" N LYS C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N HIS C 181 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU C 186 " --> pdb=" O SER C 182 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 194 removed outlier: 4.057A pdb=" N ASP C 193 " --> pdb=" O GLN C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 242 Proline residue: C 236 - end of helix Processing helix chain 'C' and resid 248 through 269 Processing helix chain 'C' and resid 283 through 304 removed outlier: 3.602A pdb=" N ARG C 288 " --> pdb=" O PRO C 284 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N MET C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE C 298 " --> pdb=" O THR C 294 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 removed outlier: 4.115A pdb=" N ASN C 310 " --> pdb=" O TYR C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 329 removed outlier: 3.646A pdb=" N LEU C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL C 329 " --> pdb=" O SER C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 342 removed outlier: 4.094A pdb=" N ARG C 339 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LYS C 340 " --> pdb=" O ARG C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 347 removed outlier: 4.565A pdb=" N TYR C 347 " --> pdb=" O HIS C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 379 removed outlier: 3.650A pdb=" N LEU C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N PHE C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 384 Processing helix chain 'C' and resid 390 through 400 Processing helix chain 'C' and resid 418 through 435 Processing helix chain 'C' and resid 446 through 473 removed outlier: 3.918A pdb=" N THR C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE C 467 " --> pdb=" O LEU C 463 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE C 468 " --> pdb=" O TYR C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 499 removed outlier: 4.876A pdb=" N ASN C 481 " --> pdb=" O GLN C 477 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR C 482 " --> pdb=" O MET C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 521 Processing helix chain 'C' and resid 524 through 532 Processing helix chain 'C' and resid 533 through 545 Processing helix chain 'C' and resid 545 through 552 Processing helix chain 'C' and resid 553 through 556 Processing helix chain 'C' and resid 559 through 570 Processing helix chain 'C' and resid 620 through 625 Processing helix chain 'C' and resid 647 through 657 Processing helix chain 'C' and resid 657 through 668 removed outlier: 3.874A pdb=" N SER C 663 " --> pdb=" O ALA C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 696 Processing helix chain 'C' and resid 704 through 706 No H-bonds generated for 'chain 'C' and resid 704 through 706' Processing helix chain 'C' and resid 707 through 722 Processing helix chain 'D' and resid 16 through 26 removed outlier: 3.996A pdb=" N ASN D 26 " --> pdb=" O VAL D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 54 Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 76 through 90 Processing helix chain 'D' and resid 146 through 158 Processing helix chain 'D' and resid 158 through 163 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 175 through 189 removed outlier: 3.846A pdb=" N LYS D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N HIS D 181 " --> pdb=" O ASN D 177 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 194 removed outlier: 4.058A pdb=" N ASP D 193 " --> pdb=" O GLN D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 242 Proline residue: D 236 - end of helix Processing helix chain 'D' and resid 248 through 269 Processing helix chain 'D' and resid 283 through 304 removed outlier: 3.602A pdb=" N ARG D 288 " --> pdb=" O PRO D 284 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N MET D 289 " --> pdb=" O LYS D 285 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 312 removed outlier: 4.115A pdb=" N ASN D 310 " --> pdb=" O TYR D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 329 removed outlier: 3.645A pdb=" N LEU D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 342 removed outlier: 4.095A pdb=" N ARG D 339 " --> pdb=" O GLY D 335 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LYS D 340 " --> pdb=" O ARG D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 347 removed outlier: 4.566A pdb=" N TYR D 347 " --> pdb=" O HIS D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 379 removed outlier: 3.649A pdb=" N LEU D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N PHE D 379 " --> pdb=" O ASP D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 384 Processing helix chain 'D' and resid 390 through 400 Processing helix chain 'D' and resid 418 through 435 Processing helix chain 'D' and resid 446 through 473 removed outlier: 3.917A pdb=" N THR D 466 " --> pdb=" O LEU D 462 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE D 467 " --> pdb=" O LEU D 463 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE D 468 " --> pdb=" O TYR D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 499 removed outlier: 4.875A pdb=" N ASN D 481 " --> pdb=" O GLN D 477 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N THR D 482 " --> pdb=" O MET D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 521 Processing helix chain 'D' and resid 524 through 532 Processing helix chain 'D' and resid 533 through 545 Processing helix chain 'D' and resid 545 through 552 Processing helix chain 'D' and resid 553 through 556 Processing helix chain 'D' and resid 559 through 570 Processing helix chain 'D' and resid 620 through 625 Processing helix chain 'D' and resid 647 through 657 Processing helix chain 'D' and resid 657 through 668 removed outlier: 3.874A pdb=" N SER D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 696 Processing helix chain 'D' and resid 704 through 706 No H-bonds generated for 'chain 'D' and resid 704 through 706' Processing helix chain 'D' and resid 707 through 722 Processing helix chain 'E' and resid 6 through 10 Processing helix chain 'E' and resid 11 through 20 removed outlier: 4.600A pdb=" N ALA E 15 " --> pdb=" O GLU E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 40 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.125A pdb=" N PHE E 68 " --> pdb=" O ASP E 64 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 93 Processing helix chain 'E' and resid 101 through 113 Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'F' and resid 6 through 10 Processing helix chain 'F' and resid 11 through 20 removed outlier: 4.599A pdb=" N ALA F 15 " --> pdb=" O GLU F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 40 Processing helix chain 'F' and resid 44 through 56 Processing helix chain 'F' and resid 64 through 77 removed outlier: 4.124A pdb=" N PHE F 68 " --> pdb=" O ASP F 64 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS F 77 " --> pdb=" O ALA F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 93 Processing helix chain 'F' and resid 101 through 113 Processing helix chain 'F' and resid 117 through 129 Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'G' and resid 6 through 10 Processing helix chain 'G' and resid 11 through 20 removed outlier: 4.600A pdb=" N ALA G 15 " --> pdb=" O GLU G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 40 Processing helix chain 'G' and resid 44 through 56 Processing helix chain 'G' and resid 64 through 77 removed outlier: 4.125A pdb=" N PHE G 68 " --> pdb=" O ASP G 64 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS G 77 " --> pdb=" O ALA G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 93 Processing helix chain 'G' and resid 101 through 113 Processing helix chain 'G' and resid 117 through 129 Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'H' and resid 6 through 10 Processing helix chain 'H' and resid 11 through 20 removed outlier: 4.599A pdb=" N ALA H 15 " --> pdb=" O GLU H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 40 Processing helix chain 'H' and resid 44 through 56 Processing helix chain 'H' and resid 64 through 77 removed outlier: 4.124A pdb=" N PHE H 68 " --> pdb=" O ASP H 64 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS H 77 " --> pdb=" O ALA H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 93 Processing helix chain 'H' and resid 101 through 113 Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 137 through 146 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 removed outlier: 6.591A pdb=" N ILE A 42 " --> pdb=" O ASN A 34 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASN A 34 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 125 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN A 93 " --> pdb=" O ILE A 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 275 removed outlier: 4.899A pdb=" N GLY A 275 " --> pdb=" O GLU A 279 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 571 through 575 removed outlier: 3.510A pdb=" N CYS A 592 " --> pdb=" O PHE A 617 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR A 672 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 580 through 582 removed outlier: 6.871A pdb=" N VAL A 634 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 609 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLN A 603 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL A 607 " --> pdb=" O GLN A 603 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 587 through 588 removed outlier: 4.355A pdb=" N ALA A 628 " --> pdb=" O VAL A 588 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 42 through 45 removed outlier: 6.591A pdb=" N ILE B 42 " --> pdb=" O ASN B 34 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASN B 34 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 125 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN B 93 " --> pdb=" O ILE B 113 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 275 removed outlier: 4.899A pdb=" N GLY B 275 " --> pdb=" O GLU B 279 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 571 through 575 removed outlier: 3.510A pdb=" N CYS B 592 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR B 672 " --> pdb=" O VAL B 616 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 580 through 582 removed outlier: 6.870A pdb=" N VAL B 634 " --> pdb=" O ILE B 581 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA B 609 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLN B 603 " --> pdb=" O VAL B 607 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL B 607 " --> pdb=" O GLN B 603 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 587 through 588 removed outlier: 4.356A pdb=" N ALA B 628 " --> pdb=" O VAL B 588 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 42 through 45 removed outlier: 6.590A pdb=" N ILE C 42 " --> pdb=" O ASN C 34 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASN C 34 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C 125 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN C 93 " --> pdb=" O ILE C 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 273 through 275 removed outlier: 4.898A pdb=" N GLY C 275 " --> pdb=" O GLU C 279 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU C 279 " --> pdb=" O GLY C 275 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 571 through 575 removed outlier: 3.510A pdb=" N CYS C 592 " --> pdb=" O PHE C 617 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR C 672 " --> pdb=" O VAL C 616 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 580 through 582 removed outlier: 6.870A pdb=" N VAL C 634 " --> pdb=" O ILE C 581 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA C 609 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLN C 603 " --> pdb=" O VAL C 607 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 587 through 588 removed outlier: 4.355A pdb=" N ALA C 628 " --> pdb=" O VAL C 588 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 42 through 45 removed outlier: 6.591A pdb=" N ILE D 42 " --> pdb=" O ASN D 34 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASN D 34 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 125 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN D 93 " --> pdb=" O ILE D 113 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 273 through 275 removed outlier: 4.899A pdb=" N GLY D 275 " --> pdb=" O GLU D 279 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU D 279 " --> pdb=" O GLY D 275 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 571 through 575 removed outlier: 3.510A pdb=" N CYS D 592 " --> pdb=" O PHE D 617 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR D 672 " --> pdb=" O VAL D 616 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 580 through 582 removed outlier: 6.871A pdb=" N VAL D 634 " --> pdb=" O ILE D 581 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA D 609 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLN D 603 " --> pdb=" O VAL D 607 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL D 607 " --> pdb=" O GLN D 603 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 587 through 588 removed outlier: 4.355A pdb=" N ALA D 628 " --> pdb=" O VAL D 588 " (cutoff:3.500A) 1572 hydrogen bonds defined for protein. 4536 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: 9.39 Time building geometry restraints manager: 10.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7950 1.34 - 1.46: 4433 1.46 - 1.58: 12409 1.58 - 1.70: 0 1.70 - 1.82: 172 Bond restraints: 24964 Sorted by residual: bond pdb=" N PHE C 359 " pdb=" CA PHE C 359 " ideal model delta sigma weight residual 1.459 1.435 0.024 1.17e-02 7.31e+03 4.25e+00 bond pdb=" N PHE B 359 " pdb=" CA PHE B 359 " ideal model delta sigma weight residual 1.459 1.436 0.023 1.17e-02 7.31e+03 3.99e+00 bond pdb=" N PHE A 359 " pdb=" CA PHE A 359 " ideal model delta sigma weight residual 1.459 1.436 0.023 1.17e-02 7.31e+03 3.97e+00 bond pdb=" N PHE D 359 " pdb=" CA PHE D 359 " ideal model delta sigma weight residual 1.459 1.436 0.023 1.17e-02 7.31e+03 3.70e+00 bond pdb=" CD1 TYR B 428 " pdb=" CE1 TYR B 428 " ideal model delta sigma weight residual 1.382 1.324 0.058 3.00e-02 1.11e+03 3.70e+00 ... (remaining 24959 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.27: 582 106.27 - 113.22: 13358 113.22 - 120.17: 8819 120.17 - 127.11: 11129 127.11 - 134.06: 276 Bond angle restraints: 34164 Sorted by residual: angle pdb=" N MET B 431 " pdb=" CA MET B 431 " pdb=" CB MET B 431 " ideal model delta sigma weight residual 110.01 102.48 7.53 1.45e+00 4.76e-01 2.70e+01 angle pdb=" N MET D 431 " pdb=" CA MET D 431 " pdb=" CB MET D 431 " ideal model delta sigma weight residual 110.01 102.48 7.53 1.45e+00 4.76e-01 2.69e+01 angle pdb=" N MET C 431 " pdb=" CA MET C 431 " pdb=" CB MET C 431 " ideal model delta sigma weight residual 110.01 102.52 7.49 1.45e+00 4.76e-01 2.67e+01 angle pdb=" N MET A 431 " pdb=" CA MET A 431 " pdb=" CB MET A 431 " ideal model delta sigma weight residual 110.01 102.53 7.48 1.45e+00 4.76e-01 2.66e+01 angle pdb=" C LYS B 450 " pdb=" CA LYS B 450 " pdb=" CB LYS B 450 " ideal model delta sigma weight residual 109.67 118.57 -8.90 2.01e+00 2.48e-01 1.96e+01 ... (remaining 34159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.64: 13283 15.64 - 31.29: 966 31.29 - 46.93: 171 46.93 - 62.57: 32 62.57 - 78.21: 28 Dihedral angle restraints: 14480 sinusoidal: 4608 harmonic: 9872 Sorted by residual: dihedral pdb=" CA TYR D 499 " pdb=" C TYR D 499 " pdb=" N GLN D 500 " pdb=" CA GLN D 500 " ideal model delta harmonic sigma weight residual 180.00 153.53 26.47 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA TYR A 499 " pdb=" C TYR A 499 " pdb=" N GLN A 500 " pdb=" CA GLN A 500 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA TYR C 499 " pdb=" C TYR C 499 " pdb=" N GLN C 500 " pdb=" CA GLN C 500 " ideal model delta harmonic sigma weight residual 180.00 153.59 26.41 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 14477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3612 0.078 - 0.156: 348 0.156 - 0.234: 28 0.234 - 0.312: 10 0.312 - 0.389: 10 Chirality restraints: 4008 Sorted by residual: chirality pdb=" CB ILE C 378 " pdb=" CA ILE C 378 " pdb=" CG1 ILE C 378 " pdb=" CG2 ILE C 378 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CB ILE D 378 " pdb=" CA ILE D 378 " pdb=" CG1 ILE D 378 " pdb=" CG2 ILE D 378 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CB ILE B 378 " pdb=" CA ILE B 378 " pdb=" CG1 ILE B 378 " pdb=" CG2 ILE B 378 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 4005 not shown) Planarity restraints: 4416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 47 " -0.018 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" CG ASP C 47 " 0.065 2.00e-02 2.50e+03 pdb=" OD1 ASP C 47 " -0.024 2.00e-02 2.50e+03 pdb=" OD2 ASP C 47 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 47 " -0.018 2.00e-02 2.50e+03 3.76e-02 1.42e+01 pdb=" CG ASP D 47 " 0.065 2.00e-02 2.50e+03 pdb=" OD1 ASP D 47 " -0.024 2.00e-02 2.50e+03 pdb=" OD2 ASP D 47 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 47 " -0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" CG ASP A 47 " 0.065 2.00e-02 2.50e+03 pdb=" OD1 ASP A 47 " -0.023 2.00e-02 2.50e+03 pdb=" OD2 ASP A 47 " -0.023 2.00e-02 2.50e+03 ... (remaining 4413 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4831 2.77 - 3.30: 27126 3.30 - 3.83: 41904 3.83 - 4.37: 46091 4.37 - 4.90: 75741 Nonbonded interactions: 195693 Sorted by model distance: nonbonded pdb=" OG SER B 418 " pdb=" OD1 ASN B 420 " model vdw 2.237 3.040 nonbonded pdb=" OG SER A 418 " pdb=" OD1 ASN A 420 " model vdw 2.237 3.040 nonbonded pdb=" OG SER C 418 " pdb=" OD1 ASN C 420 " model vdw 2.237 3.040 nonbonded pdb=" OG SER D 418 " pdb=" OD1 ASN D 420 " model vdw 2.237 3.040 nonbonded pdb=" OG SER B 25 " pdb=" OG1 THR B 28 " model vdw 2.239 3.040 ... (remaining 195688 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 66.220 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 24964 Z= 0.268 Angle : 0.785 9.468 34164 Z= 0.454 Chirality : 0.051 0.389 4008 Planarity : 0.006 0.103 4416 Dihedral : 12.186 78.213 8080 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 3340 helix: 0.25 (0.12), residues: 1928 sheet: 0.88 (0.36), residues: 172 loop : -0.21 (0.19), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 108 HIS 0.010 0.001 HIS D 364 PHE 0.058 0.004 PHE B 17 TYR 0.040 0.003 TYR D 428 ARG 0.023 0.001 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.9375 (tpp) cc_final: 0.9172 (tpp) REVERT: A 224 ILE cc_start: 0.9522 (pt) cc_final: 0.9231 (mm) REVERT: A 423 TYR cc_start: 0.8796 (t80) cc_final: 0.8410 (t80) REVERT: A 427 LEU cc_start: 0.9212 (tp) cc_final: 0.8876 (mt) REVERT: A 568 MET cc_start: 0.9272 (mmp) cc_final: 0.8953 (mmp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1229 time to fit residues: 14.4376 Evaluate side-chains 64 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.579 Evaluate side-chains 11 residues out of total 121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.106 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.1400 time to fit residues: 1.7580 Evaluate side-chains 9 residues out of total 121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 0.0870 chunk 254 optimal weight: 8.9990 chunk 141 optimal weight: 0.0030 chunk 86 optimal weight: 0.0050 chunk 171 optimal weight: 20.0000 chunk 136 optimal weight: 0.0040 chunk 263 optimal weight: 0.0170 chunk 101 optimal weight: 1.9990 chunk 160 optimal weight: 0.1980 chunk 196 optimal weight: 30.0000 chunk 305 optimal weight: 30.0000 overall best weight: 0.0232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24964 Z= 0.170 Angle : 0.602 7.831 34164 Z= 0.326 Chirality : 0.042 0.170 4008 Planarity : 0.004 0.051 4416 Dihedral : 5.064 60.722 3584 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 3340 helix: 0.71 (0.12), residues: 1960 sheet: 0.94 (0.37), residues: 172 loop : -0.14 (0.19), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 250 HIS 0.005 0.001 HIS C 486 PHE 0.019 0.002 PHE B 452 TYR 0.020 0.001 TYR C 428 ARG 0.011 0.001 ARG H 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 359 PHE cc_start: 0.9613 (t80) cc_final: 0.9350 (t80) REVERT: B 365 TRP cc_start: 0.9441 (m100) cc_final: 0.9165 (m100) REVERT: B 377 GLU cc_start: 0.9524 (tp30) cc_final: 0.9163 (tp30) REVERT: B 449 GLU cc_start: 0.9487 (mt-10) cc_final: 0.9267 (mt-10) REVERT: B 536 MET cc_start: 0.9399 (mmp) cc_final: 0.9122 (mmm) REVERT: B 568 MET cc_start: 0.9505 (mmp) cc_final: 0.9191 (mmp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1490 time to fit residues: 16.9529 Evaluate side-chains 66 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.534 Evaluate side-chains 11 residues out of total 121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.091 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0497 time to fit residues: 0.7857 Evaluate side-chains 10 residues out of total 121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 253 optimal weight: 0.0000 chunk 207 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 305 optimal weight: 6.9990 chunk 330 optimal weight: 40.0000 chunk 272 optimal weight: 0.4980 chunk 303 optimal weight: 20.0000 chunk 104 optimal weight: 0.0050 chunk 245 optimal weight: 20.0000 overall best weight: 1.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN B 470 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 24964 Z= 0.294 Angle : 0.692 11.058 34164 Z= 0.374 Chirality : 0.047 0.343 4008 Planarity : 0.006 0.093 4416 Dihedral : 5.159 60.756 3584 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.18 % Allowed : 2.16 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 3340 helix: 0.48 (0.12), residues: 1956 sheet: 0.95 (0.38), residues: 172 loop : -0.20 (0.19), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 108 HIS 0.007 0.001 HIS B 364 PHE 0.101 0.004 PHE C 468 TYR 0.046 0.003 TYR D 100 ARG 0.020 0.001 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 PHE cc_start: 0.9512 (t80) cc_final: 0.9250 (t80) REVERT: B 359 PHE cc_start: 0.9574 (t80) cc_final: 0.9365 (t80) REVERT: B 365 TRP cc_start: 0.9447 (m100) cc_final: 0.9156 (m100) REVERT: B 366 MET cc_start: 0.9033 (mmp) cc_final: 0.8560 (ptp) REVERT: B 377 GLU cc_start: 0.9537 (tp30) cc_final: 0.9172 (tp30) REVERT: B 435 THR cc_start: 0.9202 (p) cc_final: 0.8992 (p) REVERT: B 568 MET cc_start: 0.9508 (mmp) cc_final: 0.9156 (mmp) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.1381 time to fit residues: 14.4196 Evaluate side-chains 62 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.631 Evaluate side-chains 11 residues out of total 121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.097 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0520 time to fit residues: 0.7986 Evaluate side-chains 10 residues out of total 121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 800, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.3697 > 50: distance: 0 - 2: 4.452 distance: 1 - 2: 3.007 distance: 4 - 5: 4.250 distance: 5 - 6: 3.458 distance: 5 - 8: 3.715 distance: 6 - 13: 5.628 distance: 8 - 9: 5.984 distance: 9 - 10: 4.425 distance: 11 - 12: 3.591 distance: 13 - 14: 5.148 distance: 14 - 15: 7.334 distance: 14 - 17: 6.486 distance: 15 - 16: 8.614 distance: 15 - 22: 4.285 distance: 17 - 18: 5.021 distance: 18 - 19: 5.401 distance: 19 - 20: 7.813 distance: 20 - 21: 10.949 distance: 22 - 23: 5.488 distance: 23 - 24: 18.908 distance: 23 - 26: 7.763 distance: 24 - 25: 17.132 distance: 24 - 30: 18.195 distance: 26 - 27: 6.059 distance: 27 - 28: 7.735 distance: 27 - 29: 14.006 distance: 30 - 31: 11.503 distance: 31 - 32: 12.263 distance: 31 - 34: 7.080 distance: 32 - 33: 20.601 distance: 32 - 41: 11.867 distance: 34 - 35: 46.037 distance: 35 - 36: 17.032 distance: 36 - 37: 16.742 distance: 37 - 38: 12.638 distance: 38 - 39: 7.329 distance: 38 - 40: 6.786 distance: 41 - 42: 9.127 distance: 42 - 43: 10.395 distance: 42 - 45: 22.225 distance: 43 - 44: 9.831 distance: 43 - 48: 8.194 distance: 45 - 46: 22.036 distance: 45 - 47: 11.387 distance: 48 - 49: 14.463 distance: 48 - 54: 16.139 distance: 49 - 50: 8.620 distance: 49 - 52: 18.634 distance: 50 - 51: 25.020 distance: 50 - 55: 13.913 distance: 52 - 53: 26.554 distance: 53 - 54: 8.093 distance: 55 - 56: 16.911 distance: 56 - 57: 8.334 distance: 56 - 59: 9.698 distance: 57 - 58: 9.937 distance: 57 - 62: 4.268 distance: 59 - 60: 16.571 distance: 59 - 61: 21.813 distance: 62 - 63: 5.355 distance: 63 - 64: 4.771 distance: 63 - 66: 3.752 distance: 64 - 65: 3.360 distance: 66 - 67: 6.488 distance: 67 - 68: 4.002 distance: 68 - 70: 5.487 distance: 69 - 71: 4.128