Starting phenix.real_space_refine on Fri Jul 26 03:37:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9b_29863/07_2024/8g9b_29863.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9b_29863/07_2024/8g9b_29863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9b_29863/07_2024/8g9b_29863.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9b_29863/07_2024/8g9b_29863.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9b_29863/07_2024/8g9b_29863.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9b_29863/07_2024/8g9b_29863.cif" } resolution = 3.0 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= 0.242 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 96 5.49 5 S 168 5.16 5 C 19248 2.51 5 N 5344 2.21 5 O 6184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 34": "OD1" <-> "OD2" Residue "A GLU 98": "OE1" <-> "OE2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A ASP 274": "OD1" <-> "OD2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A GLU 395": "OE1" <-> "OE2" Residue "A TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 449": "OD1" <-> "OD2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 491": "OE1" <-> "OE2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B ASP 16": "OD1" <-> "OD2" Residue "B ASP 43": "OD1" <-> "OD2" Residue "B GLU 98": "OE1" <-> "OE2" Residue "B TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 255": "OD1" <-> "OD2" Residue "B ASP 256": "OD1" <-> "OD2" Residue "B ASP 261": "OD1" <-> "OD2" Residue "B ASP 269": "OD1" <-> "OD2" Residue "B ASP 292": "OD1" <-> "OD2" Residue "B ASP 315": "OD1" <-> "OD2" Residue "B ASP 319": "OD1" <-> "OD2" Residue "B GLU 395": "OE1" <-> "OE2" Residue "B ASP 418": "OD1" <-> "OD2" Residue "B GLU 487": "OE1" <-> "OE2" Residue "B GLU 500": "OE1" <-> "OE2" Residue "B GLU 510": "OE1" <-> "OE2" Residue "C ASP 15": "OD1" <-> "OD2" Residue "C ASP 16": "OD1" <-> "OD2" Residue "C ASP 71": "OD1" <-> "OD2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C GLU 98": "OE1" <-> "OE2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C ASP 232": "OD1" <-> "OD2" Residue "C GLU 254": "OE1" <-> "OE2" Residue "C ASP 256": "OD1" <-> "OD2" Residue "C ASP 274": "OD1" <-> "OD2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C ASP 418": "OD1" <-> "OD2" Residue "C ASP 449": "OD1" <-> "OD2" Residue "C ASP 470": "OD1" <-> "OD2" Residue "C GLU 491": "OE1" <-> "OE2" Residue "C GLU 510": "OE1" <-> "OE2" Residue "D ASP 15": "OD1" <-> "OD2" Residue "D ASP 34": "OD1" <-> "OD2" Residue "D ASP 71": "OD1" <-> "OD2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 274": "OD1" <-> "OD2" Residue "D GLU 352": "OE1" <-> "OE2" Residue "D GLU 395": "OE1" <-> "OE2" Residue "D PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 487": "OE1" <-> "OE2" Residue "D GLU 500": "OE1" <-> "OE2" Residue "D TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 510": "OE1" <-> "OE2" Residue "E ASP 15": "OD1" <-> "OD2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "E ASP 315": "OD1" <-> "OD2" Residue "E GLU 352": "OE1" <-> "OE2" Residue "E PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 418": "OD1" <-> "OD2" Residue "E GLU 491": "OE1" <-> "OE2" Residue "E GLU 500": "OE1" <-> "OE2" Residue "F ASP 15": "OD1" <-> "OD2" Residue "F ASP 34": "OD1" <-> "OD2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F GLU 111": "OE1" <-> "OE2" Residue "F PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 232": "OD1" <-> "OD2" Residue "F TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 254": "OE1" <-> "OE2" Residue "F GLU 335": "OE1" <-> "OE2" Residue "F GLU 395": "OE1" <-> "OE2" Residue "F PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 449": "OD1" <-> "OD2" Residue "F GLU 487": "OE1" <-> "OE2" Residue "F GLU 500": "OE1" <-> "OE2" Residue "G ASP 16": "OD1" <-> "OD2" Residue "G ASP 34": "OD1" <-> "OD2" Residue "G ASP 43": "OD1" <-> "OD2" Residue "G GLU 75": "OE1" <-> "OE2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "G ASP 117": "OD1" <-> "OD2" Residue "G GLU 168": "OE1" <-> "OE2" Residue "G GLU 254": "OE1" <-> "OE2" Residue "G ASP 256": "OD1" <-> "OD2" Residue "G ASP 292": "OD1" <-> "OD2" Residue "G ASP 315": "OD1" <-> "OD2" Residue "G ASP 319": "OD1" <-> "OD2" Residue "G GLU 335": "OE1" <-> "OE2" Residue "G GLU 352": "OE1" <-> "OE2" Residue "G PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 487": "OE1" <-> "OE2" Residue "G GLU 510": "OE1" <-> "OE2" Residue "H ASP 34": "OD1" <-> "OD2" Residue "H ASP 71": "OD1" <-> "OD2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H GLU 111": "OE1" <-> "OE2" Residue "H ASP 117": "OD1" <-> "OD2" Residue "H GLU 168": "OE1" <-> "OE2" Residue "H PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 256": "OD1" <-> "OD2" Residue "H ASP 274": "OD1" <-> "OD2" Residue "H ASP 292": "OD1" <-> "OD2" Residue "H GLU 335": "OE1" <-> "OE2" Residue "H GLU 352": "OE1" <-> "OE2" Residue "H GLU 395": "OE1" <-> "OE2" Residue "H TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 31040 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3718 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 470} Chain breaks: 1 Chain: "B" Number of atoms: 3718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3718 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 470} Chain breaks: 1 Chain: "C" Number of atoms: 3718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3718 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 470} Chain breaks: 1 Chain: "D" Number of atoms: 3718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3718 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 470} Chain breaks: 1 Chain: "E" Number of atoms: 3718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3718 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 470} Chain breaks: 1 Chain: "F" Number of atoms: 3718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3718 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 470} Chain breaks: 1 Chain: "G" Number of atoms: 3718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3718 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 470} Chain breaks: 1 Chain: "H" Number of atoms: 3718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3718 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 470} Chain breaks: 1 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Time building chain proxies: 17.25, per 1000 atoms: 0.56 Number of scatterers: 31040 At special positions: 0 Unit cell: (151.74, 151.74, 110.433, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 168 16.00 P 96 15.00 O 6184 8.00 N 5344 7.00 C 19248 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.93 Conformation dependent library (CDL) restraints added in 5.3 seconds 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7104 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 48 sheets defined 39.7% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.02 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.631A pdb=" N VAL A 49 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 85 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.749A pdb=" N VAL A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 254 through 267 removed outlier: 4.102A pdb=" N TYR A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 316 removed outlier: 3.540A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 356 removed outlier: 3.904A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 452 through 472 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 475 through 485 removed outlier: 3.578A pdb=" N ARG A 480 " --> pdb=" O LEU A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.547A pdb=" N GLN B 48 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 49 " --> pdb=" O ALA B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 45 through 49' Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 126 through 138 removed outlier: 3.721A pdb=" N VAL B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'B' and resid 255 through 267 removed outlier: 4.082A pdb=" N ARG B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 316 Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 342 through 356 removed outlier: 3.957A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 486 removed outlier: 3.552A pdb=" N ARG B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 502 Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 45 through 49 removed outlier: 3.560A pdb=" N GLN C 48 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 49 " --> pdb=" O ALA C 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 49' Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 127 through 138 removed outlier: 3.527A pdb=" N PHE C 131 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 174 through 178 removed outlier: 4.432A pdb=" N GLU C 177 " --> pdb=" O PHE C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 255 through 267 removed outlier: 4.256A pdb=" N ARG C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 316 removed outlier: 3.544A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 342 through 357 removed outlier: 3.938A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE C 357 " --> pdb=" O TYR C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 Processing helix chain 'C' and resid 416 through 420 removed outlier: 3.976A pdb=" N ALA C 419 " --> pdb=" O SER C 416 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET C 420 " --> pdb=" O LEU C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 420' Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 486 removed outlier: 3.508A pdb=" N ARG C 480 " --> pdb=" O LEU C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 45 through 49 removed outlier: 3.594A pdb=" N GLN D 48 " --> pdb=" O THR D 45 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL D 49 " --> pdb=" O ALA D 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 49' Processing helix chain 'D' and resid 76 through 85 Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 126 through 138 removed outlier: 4.054A pdb=" N VAL D 130 " --> pdb=" O ARG D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 224 through 233 Processing helix chain 'D' and resid 254 through 267 removed outlier: 4.096A pdb=" N TYR D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.590A pdb=" N MET D 286 " --> pdb=" O PHE D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 317 Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 342 through 356 removed outlier: 3.970A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 452 through 472 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 486 removed outlier: 3.567A pdb=" N ARG D 480 " --> pdb=" O LEU D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 502 Processing helix chain 'E' and resid 19 through 25 Processing helix chain 'E' and resid 45 through 49 removed outlier: 3.778A pdb=" N VAL E 49 " --> pdb=" O ALA E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 85 Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 126 through 138 Processing helix chain 'E' and resid 159 through 164 removed outlier: 3.553A pdb=" N ILE E 163 " --> pdb=" O SER E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 203 Processing helix chain 'E' and resid 224 through 233 removed outlier: 3.521A pdb=" N ARG E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 267 removed outlier: 4.093A pdb=" N TYR E 258 " --> pdb=" O GLU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 317 removed outlier: 3.815A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 342 through 357 removed outlier: 3.969A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE E 357 " --> pdb=" O TYR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 Processing helix chain 'E' and resid 416 through 420 removed outlier: 4.207A pdb=" N MET E 420 " --> pdb=" O LEU E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 486 Processing helix chain 'E' and resid 494 through 502 Processing helix chain 'F' and resid 19 through 24 Processing helix chain 'F' and resid 45 through 49 removed outlier: 3.738A pdb=" N VAL F 49 " --> pdb=" O ALA F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 85 Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 126 through 138 removed outlier: 3.867A pdb=" N VAL F 130 " --> pdb=" O ARG F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 174 through 178 removed outlier: 4.366A pdb=" N GLU F 177 " --> pdb=" O PHE F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 224 through 233 Processing helix chain 'F' and resid 255 through 267 removed outlier: 4.033A pdb=" N ARG F 259 " --> pdb=" O ASP F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 316 Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 342 through 357 removed outlier: 3.970A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE F 357 " --> pdb=" O TYR F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 452 through 472 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 486 Processing helix chain 'F' and resid 494 through 502 Processing helix chain 'G' and resid 19 through 25 Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 45 through 49 removed outlier: 3.645A pdb=" N VAL G 49 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 85 Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 127 through 138 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 193 through 205 Processing helix chain 'G' and resid 224 through 233 Processing helix chain 'G' and resid 254 through 267 removed outlier: 4.152A pdb=" N TYR G 258 " --> pdb=" O GLU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 316 Processing helix chain 'G' and resid 332 through 337 Processing helix chain 'G' and resid 342 through 356 removed outlier: 3.955A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 379 Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 485 removed outlier: 3.544A pdb=" N ARG G 480 " --> pdb=" O LEU G 476 " (cutoff:3.500A) Processing helix chain 'G' and resid 494 through 502 Processing helix chain 'H' and resid 19 through 24 Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 45 through 49 removed outlier: 3.681A pdb=" N VAL H 49 " --> pdb=" O ALA H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 85 Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 126 through 138 removed outlier: 3.796A pdb=" N VAL H 130 " --> pdb=" O ARG H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 163 Processing helix chain 'H' and resid 193 through 205 Processing helix chain 'H' and resid 224 through 233 Processing helix chain 'H' and resid 255 through 267 removed outlier: 4.177A pdb=" N ARG H 259 " --> pdb=" O ASP H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 316 Processing helix chain 'H' and resid 332 through 337 Processing helix chain 'H' and resid 342 through 356 removed outlier: 3.997A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 Processing helix chain 'H' and resid 452 through 472 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 475 through 486 Processing helix chain 'H' and resid 494 through 502 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56 removed outlier: 6.603A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.934A pdb=" N ILE A 88 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER A 67 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY A 89 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ALA A 249 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE A 91 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 320 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N MET A 385 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 145 Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 removed outlier: 6.725A pdb=" N LEU A 209 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE A 221 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE A 211 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 403 removed outlier: 3.894A pdb=" N SER D 508 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.791A pdb=" N SER A 508 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER B 444 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 37 removed outlier: 8.642A pdb=" N GLY C 29 " --> pdb=" O PHE B 490 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LYS B 492 " --> pdb=" O GLY C 29 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.977A pdb=" N ILE B 88 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 67 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE B 90 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 320 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 383 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 115 through 116 removed outlier: 6.650A pdb=" N ILE B 211 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE B 221 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU B 209 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ALA B 188 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 142 through 145 Processing sheet with id=AB4, first strand: chain 'B' and resid 508 through 510 removed outlier: 4.001A pdb=" N SER B 508 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER C 444 " --> pdb=" O GLU B 510 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 37 removed outlier: 8.284A pdb=" N GLY D 29 " --> pdb=" O PHE C 490 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LYS C 492 " --> pdb=" O GLY D 29 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.564A pdb=" N THR C 383 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C 320 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 91 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 115 through 116 removed outlier: 6.450A pdb=" N ILE C 211 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE C 221 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU C 209 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA C 188 " --> pdb=" O VAL C 212 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 142 through 145 Processing sheet with id=AC1, first strand: chain 'C' and resid 508 through 510 removed outlier: 3.742A pdb=" N SER C 508 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER D 444 " --> pdb=" O GLU C 510 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AC3, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC4, first strand: chain 'D' and resid 65 through 67 removed outlier: 4.007A pdb=" N ILE D 88 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER D 67 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLY D 89 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ALA D 249 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE D 91 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA D 320 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N MET D 385 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 142 through 145 Processing sheet with id=AC6, first strand: chain 'D' and resid 188 through 189 Processing sheet with id=AC7, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.885A pdb=" N LEU E 65 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N PHE E 90 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER E 67 " --> pdb=" O PHE E 90 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLY E 89 " --> pdb=" O GLY E 247 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ALA E 249 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE E 91 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA E 320 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N MET E 385 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 115 through 116 removed outlier: 6.436A pdb=" N ILE E 211 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE E 221 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU E 209 " --> pdb=" O ILE E 221 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 142 through 145 Processing sheet with id=AD3, first strand: chain 'E' and resid 400 through 403 removed outlier: 3.625A pdb=" N SER E 444 " --> pdb=" O GLU H 510 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER H 508 " --> pdb=" O ALA E 446 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.862A pdb=" N SER E 508 " --> pdb=" O ALA F 446 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AD6, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD7, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.930A pdb=" N ILE F 88 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER F 67 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE F 90 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA F 320 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N MET F 385 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 142 through 145 Processing sheet with id=AD9, first strand: chain 'F' and resid 188 through 189 removed outlier: 6.705A pdb=" N LEU F 209 " --> pdb=" O ILE F 221 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE F 221 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE F 211 " --> pdb=" O VAL F 219 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 508 through 510 removed outlier: 3.682A pdb=" N SER F 508 " --> pdb=" O ALA G 446 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER G 444 " --> pdb=" O GLU F 510 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AE3, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE4, first strand: chain 'G' and resid 65 through 67 removed outlier: 4.027A pdb=" N ILE G 88 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER G 67 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE G 90 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLY G 89 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ALA G 249 " --> pdb=" O GLY G 89 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE G 91 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA G 320 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR G 383 " --> pdb=" O VAL G 361 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 142 through 145 Processing sheet with id=AE6, first strand: chain 'G' and resid 188 through 189 removed outlier: 6.067A pdb=" N ALA G 188 " --> pdb=" O VAL G 212 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 508 through 510 removed outlier: 3.775A pdb=" N SER G 508 " --> pdb=" O ALA H 446 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AE9, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AF1, first strand: chain 'H' and resid 65 through 67 removed outlier: 3.947A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER H 67 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE H 90 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLY H 89 " --> pdb=" O GLY H 247 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ALA H 249 " --> pdb=" O GLY H 89 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE H 91 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA H 320 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N MET H 385 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 115 through 116 removed outlier: 6.607A pdb=" N ILE H 211 " --> pdb=" O VAL H 219 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ILE H 221 " --> pdb=" O LEU H 209 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU H 209 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA H 188 " --> pdb=" O VAL H 212 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 142 through 145 1206 hydrogen bonds defined for protein. 3390 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: 11.67 Time building geometry restraints manager: 14.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5156 1.31 - 1.43: 7776 1.43 - 1.56: 18228 1.56 - 1.69: 160 1.69 - 1.82: 272 Bond restraints: 31592 Sorted by residual: bond pdb=" C4 ATP H 603 " pdb=" C5 ATP H 603 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.03e+01 bond pdb=" C4 ATP G 603 " pdb=" C5 ATP G 603 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.00e+01 bond pdb=" C4 ATP A 603 " pdb=" C5 ATP A 603 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.95e+01 bond pdb=" C4 ATP D 603 " pdb=" C5 ATP D 603 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.95e+01 bond pdb=" C4 ATP F 603 " pdb=" C5 ATP F 603 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.83e+01 ... (remaining 31587 not shown) Histogram of bond angle deviations from ideal: 98.19 - 106.02: 821 106.02 - 113.84: 18416 113.84 - 121.67: 16605 121.67 - 129.49: 6900 129.49 - 137.32: 162 Bond angle restraints: 42904 Sorted by residual: angle pdb=" PB ATP C 603 " pdb=" O3B ATP C 603 " pdb=" PG ATP C 603 " ideal model delta sigma weight residual 139.87 109.96 29.91 1.00e+00 1.00e+00 8.94e+02 angle pdb=" PB ATP B 603 " pdb=" O3B ATP B 603 " pdb=" PG ATP B 603 " ideal model delta sigma weight residual 139.87 112.44 27.43 1.00e+00 1.00e+00 7.52e+02 angle pdb=" PA ATP C 603 " pdb=" O3A ATP C 603 " pdb=" PB ATP C 603 " ideal model delta sigma weight residual 136.83 112.04 24.79 1.00e+00 1.00e+00 6.14e+02 angle pdb=" PB ATP E 603 " pdb=" O3B ATP E 603 " pdb=" PG ATP E 603 " ideal model delta sigma weight residual 139.87 120.46 19.41 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PB ATP A 603 " pdb=" O3B ATP A 603 " pdb=" PG ATP A 603 " ideal model delta sigma weight residual 139.87 120.48 19.39 1.00e+00 1.00e+00 3.76e+02 ... (remaining 42899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.67: 18532 35.67 - 71.34: 735 71.34 - 107.01: 72 107.01 - 142.67: 37 142.67 - 178.34: 24 Dihedral angle restraints: 19400 sinusoidal: 8280 harmonic: 11120 Sorted by residual: dihedral pdb=" O3A GTP D 601 " pdb=" O3B GTP D 601 " pdb=" PB GTP D 601 " pdb=" PG GTP D 601 " ideal model delta sinusoidal sigma weight residual -56.21 122.14 -178.34 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O3B GTP E 602 " pdb=" O3A GTP E 602 " pdb=" PB GTP E 602 " pdb=" PA GTP E 602 " ideal model delta sinusoidal sigma weight residual 291.08 113.13 177.95 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' IMP F 604 " pdb=" O5' IMP F 604 " pdb=" P IMP F 604 " pdb=" O2P IMP F 604 " ideal model delta sinusoidal sigma weight residual 191.93 16.12 175.81 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 19397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4095 0.069 - 0.138: 693 0.138 - 0.207: 70 0.207 - 0.276: 12 0.276 - 0.346: 2 Chirality restraints: 4872 Sorted by residual: chirality pdb=" CA PHE A 114 " pdb=" N PHE A 114 " pdb=" C PHE A 114 " pdb=" CB PHE A 114 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA LYS H 206 " pdb=" N LYS H 206 " pdb=" C LYS H 206 " pdb=" CB LYS H 206 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA LYS B 208 " pdb=" N LYS B 208 " pdb=" C LYS B 208 " pdb=" CB LYS B 208 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 4869 not shown) Planarity restraints: 5336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 233 " 0.062 5.00e-02 4.00e+02 9.22e-02 1.36e+01 pdb=" N PRO D 234 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO D 234 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO D 234 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 231 " -0.306 9.50e-02 1.11e+02 1.37e-01 1.20e+01 pdb=" NE ARG B 231 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG B 231 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 231 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 231 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 209 " -0.055 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO B 210 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 210 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 210 " -0.045 5.00e-02 4.00e+02 ... (remaining 5333 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 149 2.49 - 3.09: 21415 3.09 - 3.69: 47866 3.69 - 4.30: 71763 4.30 - 4.90: 119217 Nonbonded interactions: 260410 Sorted by model distance: nonbonded pdb=" OG SER C 159 " pdb=" O2A ATP C 603 " model vdw 1.886 2.440 nonbonded pdb=" CB SER C 159 " pdb=" O2A ATP C 603 " model vdw 1.960 3.440 nonbonded pdb=" SG CYS C 331 " pdb=" N3 IMP C 604 " model vdw 2.023 2.784 nonbonded pdb=" O3' GTP D 602 " pdb=" O3G GTP D 602 " model vdw 2.053 2.440 nonbonded pdb=" OG SER F 204 " pdb=" CG LYS F 206 " model vdw 2.158 3.440 ... (remaining 260405 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.940 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: 0.030 Extract box with map and model: 1.220 Check model and map are aligned: 0.240 Set scattering table: 0.310 Process input model: 81.110 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.160 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:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 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 : 0.007 0.142 31592 Z= 0.490 Angle : 1.093 29.907 42904 Z= 0.648 Chirality : 0.051 0.346 4872 Planarity : 0.006 0.137 5336 Dihedral : 20.265 178.344 12296 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.99 % Favored : 95.85 % Rotamer: Outliers : 0.60 % Allowed : 14.82 % Favored : 84.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -0.04 (0.13), residues: 3880 helix: 1.15 (0.14), residues: 1400 sheet: -0.26 (0.22), residues: 432 loop : -0.78 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 171 PHE 0.016 0.001 PHE D 401 TYR 0.016 0.001 TYR H 233 ARG 0.014 0.001 ARG H 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 521 time to evaluate : 3.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.7725 (tptt) cc_final: 0.7002 (tppt) REVERT: A 261 ASP cc_start: 0.7784 (m-30) cc_final: 0.7541 (m-30) REVERT: A 420 MET cc_start: 0.4224 (tpp) cc_final: 0.4016 (tpp) REVERT: B 112 GLN cc_start: 0.7568 (pt0) cc_final: 0.7341 (pm20) REVERT: B 195 LYS cc_start: 0.7869 (tptt) cc_final: 0.7189 (tppt) REVERT: B 233 TYR cc_start: 0.8432 (m-80) cc_final: 0.7782 (m-80) REVERT: B 288 LYS cc_start: 0.7734 (mttm) cc_final: 0.7499 (mtmp) REVERT: B 410 LYS cc_start: 0.6832 (mtpt) cc_final: 0.6560 (pmtt) REVERT: C 75 GLU cc_start: 0.6974 (tt0) cc_final: 0.6760 (tt0) REVERT: C 206 LYS cc_start: 0.7286 (mmmt) cc_final: 0.6657 (mmmt) REVERT: C 335 GLU cc_start: 0.7625 (tt0) cc_final: 0.7337 (tt0) REVERT: C 410 LYS cc_start: 0.6753 (mtmt) cc_final: 0.6513 (pmtt) REVERT: C 500 GLU cc_start: 0.7991 (tt0) cc_final: 0.7609 (tt0) REVERT: D 195 LYS cc_start: 0.7783 (tptt) cc_final: 0.7187 (tppt) REVERT: D 265 GLN cc_start: 0.7963 (tt0) cc_final: 0.7669 (tt0) REVERT: D 335 GLU cc_start: 0.7569 (tt0) cc_final: 0.7316 (tt0) REVERT: D 410 LYS cc_start: 0.7007 (mtpt) cc_final: 0.6596 (pmtt) REVERT: D 483 MET cc_start: 0.9582 (tmm) cc_final: 0.9332 (tmm) REVERT: D 500 GLU cc_start: 0.8138 (tt0) cc_final: 0.7709 (tt0) REVERT: E 195 LYS cc_start: 0.7896 (tptt) cc_final: 0.7190 (tppt) REVERT: E 265 GLN cc_start: 0.7984 (tt0) cc_final: 0.7615 (mp10) REVERT: F 18 LEU cc_start: 0.9264 (mt) cc_final: 0.8982 (mp) REVERT: F 195 LYS cc_start: 0.7930 (tptm) cc_final: 0.7405 (tppt) REVERT: F 491 GLU cc_start: 0.8389 (tp30) cc_final: 0.8100 (tp30) REVERT: G 48 GLN cc_start: 0.8338 (mt0) cc_final: 0.8074 (mt0) REVERT: G 208 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8198 (mttp) REVERT: G 265 GLN cc_start: 0.7988 (tt0) cc_final: 0.7627 (tp40) REVERT: G 335 GLU cc_start: 0.7645 (tt0) cc_final: 0.7321 (tt0) REVERT: H 195 LYS cc_start: 0.7904 (tptm) cc_final: 0.7171 (tppt) REVERT: H 261 ASP cc_start: 0.7717 (m-30) cc_final: 0.7484 (m-30) REVERT: H 412 ARG cc_start: 0.7115 (ptt180) cc_final: 0.6878 (ptt90) REVERT: H 420 MET cc_start: 0.4589 (tpp) cc_final: 0.4002 (ptp) outliers start: 19 outliers final: 8 residues processed: 537 average time/residue: 1.2322 time to fit residues: 797.1217 Evaluate side-chains 496 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 487 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain G residue 161 ARG Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 208 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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: 71.1023 > 50: distance: 8 - 13: 32.582 distance: 13 - 14: 53.086 distance: 14 - 15: 58.288 distance: 14 - 17: 40.488 distance: 15 - 16: 29.546 distance: 15 - 20: 39.263 distance: 17 - 18: 41.930 distance: 17 - 19: 40.900 distance: 20 - 21: 35.392 distance: 21 - 22: 37.225 distance: 21 - 24: 45.809 distance: 22 - 23: 24.022 distance: 22 - 28: 40.795 distance: 24 - 25: 41.739 distance: 25 - 26: 8.393 distance: 25 - 27: 47.757 distance: 28 - 29: 50.732 distance: 29 - 30: 39.995 distance: 29 - 32: 64.809 distance: 30 - 31: 16.289 distance: 30 - 34: 47.307 distance: 32 - 33: 3.658 distance: 34 - 35: 52.438 distance: 34 - 40: 49.161 distance: 35 - 36: 27.429 distance: 35 - 38: 55.815 distance: 36 - 37: 13.324 distance: 36 - 41: 17.004 distance: 38 - 39: 35.616 distance: 39 - 40: 44.613 distance: 41 - 42: 4.585 distance: 42 - 43: 3.571 distance: 42 - 45: 24.522 distance: 43 - 44: 12.761 distance: 43 - 50: 53.379 distance: 45 - 46: 10.579 distance: 46 - 47: 6.642 distance: 47 - 48: 17.491 distance: 48 - 49: 7.523 distance: 50 - 51: 19.196 distance: 51 - 52: 48.905 distance: 51 - 54: 43.218 distance: 52 - 58: 24.827 distance: 54 - 55: 13.581 distance: 55 - 56: 53.328 distance: 55 - 57: 10.772 distance: 58 - 59: 15.523 distance: 59 - 60: 61.354 distance: 59 - 62: 40.079 distance: 60 - 61: 50.519 distance: 60 - 69: 41.443 distance: 62 - 63: 45.933 distance: 63 - 64: 21.665 distance: 64 - 65: 23.537 distance: 65 - 66: 11.435 distance: 66 - 67: 11.303 distance: 66 - 68: 7.253 distance: 69 - 70: 11.022 distance: 70 - 71: 64.033 distance: 71 - 72: 41.009 distance: 71 - 76: 9.767 distance: 72 - 102: 33.926 distance: 73 - 74: 69.674 distance: 73 - 75: 41.488 distance: 76 - 77: 38.615 distance: 77 - 78: 14.731 distance: 77 - 80: 20.738 distance: 78 - 79: 34.935 distance: 78 - 87: 30.952 distance: 79 - 110: 35.114 distance: 80 - 81: 34.132 distance: 81 - 82: 32.402 distance: 82 - 83: 6.868 distance: 83 - 84: 14.683 distance: 84 - 85: 17.824 distance: 84 - 86: 12.100 distance: 87 - 88: 33.543 distance: 88 - 89: 36.616 distance: 88 - 91: 8.970 distance: 89 - 90: 18.635 distance: 89 - 95: 32.409 distance: 90 - 119: 29.057 distance: 91 - 92: 51.169 distance: 92 - 93: 25.713 distance: 92 - 94: 18.377