Starting phenix.real_space_refine on Thu Sep 26 10:51:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgm_24452/09_2024/7rgm_24452_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgm_24452/09_2024/7rgm_24452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgm_24452/09_2024/7rgm_24452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgm_24452/09_2024/7rgm_24452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgm_24452/09_2024/7rgm_24452_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgm_24452/09_2024/7rgm_24452_trim.cif" } resolution = 2.8 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= 0.278 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 72 5.49 5 S 192 5.16 5 C 18840 2.51 5 N 5160 2.21 5 O 5928 1.98 5 H 29736 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 285 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 59928 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 7362 Classifications: {'peptide': 484} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 465} Chain breaks: 2 Chain: "B" Number of atoms: 7362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 7362 Classifications: {'peptide': 484} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 465} Chain breaks: 2 Chain: "C" Number of atoms: 7362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 7362 Classifications: {'peptide': 484} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 465} Chain breaks: 2 Chain: "D" Number of atoms: 7362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 7362 Classifications: {'peptide': 484} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 465} Chain breaks: 2 Chain: "E" Number of atoms: 7362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 7362 Classifications: {'peptide': 484} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 465} Chain breaks: 2 Chain: "F" Number of atoms: 7362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 7362 Classifications: {'peptide': 484} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 465} Chain breaks: 2 Chain: "G" Number of atoms: 7362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 7362 Classifications: {'peptide': 484} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 465} Chain breaks: 2 Chain: "H" Number of atoms: 7362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 7362 Classifications: {'peptide': 484} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 465} Chain breaks: 2 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "G" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 24.33, per 1000 atoms: 0.41 Number of scatterers: 59928 At special positions: 0 Unit cell: (146.682, 145.839, 130.665, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 192 16.00 P 72 15.00 O 5928 8.00 N 5160 7.00 C 18840 6.00 H 29736 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.38 Conformation dependent library (CDL) restraints added in 3.7 seconds 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6960 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 49 sheets defined 39.8% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.51 Creating SS restraints... Processing helix chain 'A' and resid 19 through 24 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.602A pdb=" N VAL A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 Processing helix chain 'A' and resid 193 through 205 removed outlier: 3.528A pdb=" N ALA A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.755A pdb=" N ARG A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 316 Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 342 through 356 removed outlier: 3.989A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.727A pdb=" N VAL A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 126 through 138 removed outlier: 3.944A pdb=" N VAL B 130 " --> pdb=" O THR B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 164 Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 255 through 266 removed outlier: 3.624A pdb=" N ARG B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP B 261 " --> pdb=" O LYS B 257 " (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 338 Processing helix chain 'B' and resid 342 through 356 removed outlier: 3.987A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 removed outlier: 3.744A pdb=" N VAL B 373 " --> pdb=" O THR B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 501 Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 126 through 138 removed outlier: 3.827A pdb=" N VAL C 130 " --> pdb=" O THR C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 224 through 229 Processing helix chain 'C' and resid 254 through 266 removed outlier: 4.256A pdb=" N TYR C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 316 Processing helix chain 'C' and resid 332 through 338 Processing helix chain 'C' and resid 342 through 356 removed outlier: 3.982A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 removed outlier: 3.739A pdb=" N VAL C 373 " --> pdb=" O THR C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 494 through 501 Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 75 through 86 Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 126 through 138 removed outlier: 3.893A pdb=" N VAL D 130 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 254 through 266 removed outlier: 4.561A pdb=" N TYR D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG D 259 " --> pdb=" O ASP D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 316 Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 342 through 356 removed outlier: 3.982A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 removed outlier: 3.735A pdb=" N VAL D 373 " --> pdb=" O THR D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 Processing helix chain 'D' and resid 452 through 472 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 501 Processing helix chain 'E' and resid 19 through 24 Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 75 through 86 Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 126 through 138 removed outlier: 3.820A pdb=" N VAL E 130 " --> pdb=" O THR E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 224 through 229 Processing helix chain 'E' and resid 255 through 266 removed outlier: 3.792A pdb=" N ARG E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 316 Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 342 through 356 removed outlier: 3.991A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 removed outlier: 3.741A pdb=" N VAL E 373 " --> pdb=" O THR E 369 " (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 485 Processing helix chain 'E' and resid 494 through 501 Processing helix chain 'F' and resid 19 through 24 Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 45 through 49 Processing helix chain 'F' and resid 75 through 86 Processing helix chain 'F' and resid 96 through 110 Processing helix chain 'F' and resid 126 through 138 removed outlier: 3.798A pdb=" N VAL F 130 " --> pdb=" O THR F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 224 through 229 Processing helix chain 'F' and resid 255 through 266 removed outlier: 3.846A 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 338 Processing helix chain 'F' and resid 342 through 356 removed outlier: 3.986A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 removed outlier: 3.740A pdb=" N VAL F 373 " --> pdb=" O THR F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 421 Processing helix chain 'F' and resid 452 through 472 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 501 Processing helix chain 'G' and resid 19 through 24 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 Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 96 through 110 Processing helix chain 'G' and resid 126 through 138 removed outlier: 3.848A pdb=" N VAL G 130 " --> pdb=" O THR G 126 " (cutoff:3.500A) 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 229 Processing helix chain 'G' and resid 255 through 266 removed outlier: 3.816A pdb=" N ARG G 259 " --> pdb=" O ASP G 255 " (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 338 Processing helix chain 'G' and resid 342 through 356 removed outlier: 3.983A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 379 removed outlier: 3.729A pdb=" N VAL G 373 " --> pdb=" O THR G 369 " (cutoff:3.500A) 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 Processing helix chain 'G' and resid 494 through 501 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 Processing helix chain 'H' and resid 75 through 86 Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 126 through 138 removed outlier: 3.821A pdb=" N VAL H 130 " --> pdb=" O THR H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 164 Processing helix chain 'H' and resid 183 through 185 No H-bonds generated for 'chain 'H' and resid 183 through 185' Processing helix chain 'H' and resid 193 through 205 Processing helix chain 'H' and resid 224 through 229 Processing helix chain 'H' and resid 255 through 266 removed outlier: 4.196A 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 338 Processing helix chain 'H' and resid 342 through 356 removed outlier: 3.984A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 removed outlier: 3.730A pdb=" N VAL H 373 " --> pdb=" O THR H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 472 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 494 through 501 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 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.567A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLY A 89 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ALA A 249 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE A 91 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE A 271 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N GLY A 302 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU A 273 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N VAL A 304 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL A 299 " --> pdb=" O GLY A 320 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ARG A 322 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY A 301 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 383 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE A 66 " --> pdb=" O MET A 386 " (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 208 through 212 Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 402 Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.574A pdb=" N PHE B 90 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLY B 89 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ALA B 249 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE B 91 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE B 271 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N GLY B 302 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU B 273 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N VAL B 304 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLY B 320 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLY B 302 " --> pdb=" O GLY B 320 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG B 322 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 383 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 142 through 145 Processing sheet with id=AB2, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.865A pdb=" N SER B 152 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 208 through 211 Processing sheet with id=AB4, first strand: chain 'B' and resid 401 through 403 Processing sheet with id=AB5, first strand: chain 'B' and resid 508 through 510 removed outlier: 3.889A pdb=" N SER B 508 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N SER C 444 " --> pdb=" O THR B 510 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB7, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB8, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.792A pdb=" N PHE C 90 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY C 89 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ALA C 249 " --> pdb=" O GLY C 89 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE C 91 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLY C 320 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N GLY C 302 " --> pdb=" O GLY C 320 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ARG C 322 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR C 383 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE C 66 " --> pdb=" O MET C 386 " (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 208 through 212 Processing sheet with id=AC2, first strand: chain 'C' and resid 508 through 509 removed outlier: 3.937A pdb=" N SER C 508 " --> pdb=" O SER D 446 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AC4, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC5, first strand: chain 'D' and resid 65 through 67 removed outlier: 3.640A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY D 89 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ALA D 249 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE D 91 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE D 271 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N GLY D 302 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU D 273 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N VAL D 304 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY D 320 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N GLY D 302 " --> pdb=" O GLY D 320 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ARG D 322 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR D 383 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE D 66 " --> pdb=" O MET D 386 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 142 through 145 Processing sheet with id=AC7, first strand: chain 'D' and resid 208 through 212 Processing sheet with id=AC8, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AC9, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AD1, first strand: chain 'E' and resid 65 through 67 removed outlier: 3.619A pdb=" N PHE E 90 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLY E 89 " --> pdb=" O GLY E 247 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ALA E 249 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE E 91 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE E 271 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N GLY E 302 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU E 273 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N VAL E 304 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY E 320 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLY E 302 " --> pdb=" O GLY E 320 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG E 322 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR E 383 " --> pdb=" O ILE E 361 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE E 66 " --> pdb=" O MET E 386 " (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 208 through 212 Processing sheet with id=AD4, first strand: chain 'E' and resid 401 through 403 Processing sheet with id=AD5, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.911A pdb=" N SER E 508 " --> pdb=" O SER F 446 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER F 444 " --> pdb=" O THR E 510 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AD7, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD8, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.601A pdb=" N PHE F 90 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY F 89 " --> pdb=" O GLY F 247 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ALA F 249 " --> pdb=" O GLY F 89 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE F 91 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE F 271 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N GLY F 302 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU F 273 " --> pdb=" O GLY F 302 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N VAL F 304 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY F 320 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLY F 302 " --> pdb=" O GLY F 320 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG F 322 " --> pdb=" O GLY F 302 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR F 383 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 142 through 145 Processing sheet with id=AE1, first strand: chain 'F' and resid 188 through 189 removed outlier: 6.268A pdb=" N ALA F 188 " --> pdb=" O VAL F 212 " (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: 3.510A pdb=" N PHE G 90 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY G 89 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ALA G 249 " --> pdb=" O GLY G 89 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE G 91 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA G 248 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE G 271 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N GLY G 302 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU G 273 " --> pdb=" O GLY G 302 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N VAL G 304 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY G 320 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N GLY G 302 " --> pdb=" O GLY G 320 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG G 322 " --> pdb=" O GLY G 302 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR G 383 " --> pdb=" O ILE G 361 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 142 through 145 removed outlier: 3.506A pdb=" N GLY G 156 " --> pdb=" O ILE G 144 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 208 through 211 Processing sheet with id=AE7, first strand: chain 'G' and resid 401 through 402 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: 3.507A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE H 90 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLY H 89 " --> pdb=" O GLY H 247 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ALA H 249 " --> pdb=" O GLY H 89 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE H 91 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE H 271 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N GLY H 302 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU H 273 " --> pdb=" O GLY H 302 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL H 304 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLY H 320 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N GLY H 302 " --> pdb=" O GLY H 320 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG H 322 " --> pdb=" O GLY H 302 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR H 383 " --> pdb=" O ILE H 361 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE H 66 " --> pdb=" O MET H 386 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 142 through 145 removed outlier: 3.562A pdb=" N GLY H 156 " --> pdb=" O ILE H 144 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 208 through 211 Processing sheet with id=AF4, first strand: chain 'H' and resid 401 through 403 1143 hydrogen bonds defined for protein. 3213 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: 23.02 Time building geometry restraints manager: 14.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 29680 1.12 - 1.29: 5018 1.29 - 1.47: 11156 1.47 - 1.65: 14266 1.65 - 1.82: 328 Bond restraints: 60448 Sorted by residual: bond pdb=" NE ARG B 57 " pdb=" HE ARG B 57 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ILE C 157 " pdb=" H ILE C 157 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ILE F 221 " pdb=" H ILE F 221 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ALA A 81 " pdb=" H ALA A 81 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NH1 ARG G 412 " pdb="HH11 ARG G 412 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 60443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 101166 3.77 - 7.55: 7883 7.55 - 11.32: 232 11.32 - 15.09: 47 15.09 - 18.86: 16 Bond angle restraints: 109344 Sorted by residual: angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 121.01 18.86 1.00e+00 1.00e+00 3.56e+02 angle pdb=" PB ATP E 602 " pdb=" O3B ATP E 602 " pdb=" PG ATP E 602 " ideal model delta sigma weight residual 139.87 121.09 18.78 1.00e+00 1.00e+00 3.53e+02 angle pdb=" PB ATP F 602 " pdb=" O3B ATP F 602 " pdb=" PG ATP F 602 " ideal model delta sigma weight residual 139.87 121.66 18.21 1.00e+00 1.00e+00 3.32e+02 angle pdb=" PB ATP H 602 " pdb=" O3B ATP H 602 " pdb=" PG ATP H 602 " ideal model delta sigma weight residual 139.87 121.96 17.91 1.00e+00 1.00e+00 3.21e+02 angle pdb=" PB ATP D 602 " pdb=" O3B ATP D 602 " pdb=" PG ATP D 602 " ideal model delta sigma weight residual 139.87 122.08 17.79 1.00e+00 1.00e+00 3.17e+02 ... (remaining 109339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.23: 25890 24.23 - 48.47: 1855 48.47 - 72.70: 916 72.70 - 96.93: 94 96.93 - 121.16: 5 Dihedral angle restraints: 28760 sinusoidal: 16488 harmonic: 12272 Sorted by residual: dihedral pdb=" C5' IMP H 603 " pdb=" O5' IMP H 603 " pdb=" P IMP H 603 " pdb=" O2P IMP H 603 " ideal model delta sinusoidal sigma weight residual 191.93 70.77 121.16 1 2.00e+01 2.50e-03 3.64e+01 dihedral pdb=" C5' IMP G 603 " pdb=" O5' IMP G 603 " pdb=" P IMP G 603 " pdb=" O2P IMP G 603 " ideal model delta sinusoidal sigma weight residual -168.07 -47.50 -120.57 1 2.00e+01 2.50e-03 3.62e+01 dihedral pdb=" C5' IMP D 603 " pdb=" O5' IMP D 603 " pdb=" P IMP D 603 " pdb=" O2P IMP D 603 " ideal model delta sinusoidal sigma weight residual -168.07 -54.66 -113.41 1 2.00e+01 2.50e-03 3.35e+01 ... (remaining 28757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3142 0.072 - 0.145: 1275 0.145 - 0.217: 333 0.217 - 0.290: 83 0.290 - 0.362: 7 Chirality restraints: 4840 Sorted by residual: chirality pdb=" CA ASP C 216 " pdb=" N ASP C 216 " pdb=" C ASP C 216 " pdb=" CB ASP C 216 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA ASP B 216 " pdb=" N ASP B 216 " pdb=" C ASP B 216 " pdb=" CB ASP B 216 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CA ASP H 216 " pdb=" N ASP H 216 " pdb=" C ASP H 216 " pdb=" CB ASP H 216 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 4837 not shown) Planarity restraints: 8888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' IMP G 603 " -0.140 2.00e-02 2.50e+03 1.08e-01 2.89e+02 pdb=" C2 IMP G 603 " 0.182 2.00e-02 2.50e+03 pdb=" C4 IMP G 603 " -0.040 2.00e-02 2.50e+03 pdb=" C5 IMP G 603 " -0.027 2.00e-02 2.50e+03 pdb=" C6 IMP G 603 " -0.158 2.00e-02 2.50e+03 pdb=" C8 IMP G 603 " 0.109 2.00e-02 2.50e+03 pdb=" N1 IMP G 603 " -0.084 2.00e-02 2.50e+03 pdb=" N3 IMP G 603 " 0.074 2.00e-02 2.50e+03 pdb=" N7 IMP G 603 " 0.105 2.00e-02 2.50e+03 pdb=" N9 IMP G 603 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 161 " 0.069 9.50e-02 1.11e+02 1.06e-01 2.39e+02 pdb=" NE ARG E 161 " 0.099 2.00e-02 2.50e+03 pdb=" CZ ARG E 161 " 0.083 2.00e-02 2.50e+03 pdb=" NH1 ARG E 161 " 0.043 2.00e-02 2.50e+03 pdb=" NH2 ARG E 161 " 0.074 2.00e-02 2.50e+03 pdb="HH11 ARG E 161 " -0.173 2.00e-02 2.50e+03 pdb="HH12 ARG E 161 " 0.033 2.00e-02 2.50e+03 pdb="HH21 ARG E 161 " -0.198 2.00e-02 2.50e+03 pdb="HH22 ARG E 161 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 161 " -0.040 9.50e-02 1.11e+02 8.87e-02 1.73e+02 pdb=" NE ARG G 161 " 0.054 2.00e-02 2.50e+03 pdb=" CZ ARG G 161 " 0.085 2.00e-02 2.50e+03 pdb=" NH1 ARG G 161 " 0.071 2.00e-02 2.50e+03 pdb=" NH2 ARG G 161 " 0.088 2.00e-02 2.50e+03 pdb="HH11 ARG G 161 " -0.143 2.00e-02 2.50e+03 pdb="HH12 ARG G 161 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG G 161 " -0.161 2.00e-02 2.50e+03 pdb="HH22 ARG G 161 " 0.006 2.00e-02 2.50e+03 ... (remaining 8885 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.05: 2101 2.05 - 2.69: 84578 2.69 - 3.33: 183070 3.33 - 3.96: 246741 3.96 - 4.60: 367846 Nonbonded interactions: 884336 Sorted by model distance: nonbonded pdb=" HA LYS G 455 " pdb=" HD3 LYS G 455 " model vdw 1.417 2.440 nonbonded pdb=" HA LYS A 455 " pdb=" HD3 LYS A 455 " model vdw 1.424 2.440 nonbonded pdb=" HA LYS C 455 " pdb=" HD3 LYS C 455 " model vdw 1.425 2.440 nonbonded pdb=" HB2 GLN A 283 " pdb="HE21 GLN A 283 " model vdw 1.476 2.270 nonbonded pdb=" HB2 GLN B 283 " pdb="HE21 GLN B 283 " model vdw 1.480 2.270 ... (remaining 884331 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' 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: 4.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.790 Extract box with map and model: 1.670 Check model and map are aligned: 0.360 Set scattering table: 0.420 Process input model: 102.410 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.790 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 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 : 0.014 0.102 30712 Z= 0.908 Angle : 1.693 18.864 41680 Z= 1.128 Chirality : 0.084 0.362 4840 Planarity : 0.011 0.108 5176 Dihedral : 17.170 121.163 12000 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.18 % Favored : 94.56 % Rotamer: Outliers : 3.63 % Allowed : 9.48 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.12), residues: 3824 helix: -1.38 (0.11), residues: 1496 sheet: -0.26 (0.30), residues: 192 loop : -1.05 (0.12), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 466 PHE 0.081 0.011 PHE B 44 TYR 0.143 0.011 TYR E 400 ARG 0.012 0.001 ARG B 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 639 time to evaluate : 3.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8803 (m) REVERT: A 105 ARG cc_start: 0.8238 (ttp80) cc_final: 0.7953 (ttp80) REVERT: A 140 SER cc_start: 0.7979 (t) cc_final: 0.7777 (p) REVERT: A 292 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7281 (tm130) REVERT: A 293 LYS cc_start: 0.8303 (tttp) cc_final: 0.8080 (tttm) REVERT: A 325 MET cc_start: 0.9333 (ttt) cc_final: 0.9031 (ttt) REVERT: A 412 ARG cc_start: 0.7319 (ptt180) cc_final: 0.7067 (ptt-90) REVERT: A 456 PHE cc_start: 0.8765 (t80) cc_final: 0.8522 (t80) REVERT: A 459 TYR cc_start: 0.7874 (t80) cc_final: 0.7472 (t80) REVERT: B 62 LYS cc_start: 0.8423 (mmtp) cc_final: 0.8171 (mmmt) REVERT: B 63 THR cc_start: 0.9086 (OUTLIER) cc_final: 0.8838 (m) REVERT: B 112 GLN cc_start: 0.6915 (tt0) cc_final: 0.6705 (mp10) REVERT: B 206 LYS cc_start: 0.8012 (mmtt) cc_final: 0.7731 (mmmt) REVERT: B 269 ASP cc_start: 0.7769 (m-30) cc_final: 0.7559 (m-30) REVERT: B 292 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7300 (tm130) REVERT: B 293 LYS cc_start: 0.8302 (tttp) cc_final: 0.8093 (tttm) REVERT: B 325 MET cc_start: 0.9307 (ttt) cc_final: 0.8995 (ttt) REVERT: B 330 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8507 (pp) REVERT: B 412 ARG cc_start: 0.7896 (ptt180) cc_final: 0.7507 (ptt180) REVERT: B 459 TYR cc_start: 0.7934 (t80) cc_final: 0.7493 (t80) REVERT: C 63 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8844 (m) REVERT: C 292 GLN cc_start: 0.7999 (tm-30) cc_final: 0.7287 (tm130) REVERT: C 293 LYS cc_start: 0.8261 (tttp) cc_final: 0.8030 (tttm) REVERT: C 325 MET cc_start: 0.9313 (ttt) cc_final: 0.8998 (ttt) REVERT: C 412 ARG cc_start: 0.8006 (ptt180) cc_final: 0.7584 (ptt180) REVERT: C 456 PHE cc_start: 0.8843 (t80) cc_final: 0.8606 (t80) REVERT: C 459 TYR cc_start: 0.7835 (t80) cc_final: 0.7562 (t80) REVERT: D 63 THR cc_start: 0.9091 (OUTLIER) cc_final: 0.8828 (m) REVERT: D 112 GLN cc_start: 0.6988 (tt0) cc_final: 0.6704 (mp10) REVERT: D 269 ASP cc_start: 0.7755 (m-30) cc_final: 0.7512 (m-30) REVERT: D 292 GLN cc_start: 0.8080 (tm-30) cc_final: 0.7351 (tm130) REVERT: D 325 MET cc_start: 0.9323 (ttt) cc_final: 0.9012 (ttt) REVERT: D 412 ARG cc_start: 0.8065 (ptt180) cc_final: 0.7754 (ptt180) REVERT: D 456 PHE cc_start: 0.8799 (t80) cc_final: 0.8503 (t80) REVERT: D 459 TYR cc_start: 0.7958 (t80) cc_final: 0.7529 (t80) REVERT: D 470 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7779 (m-30) REVERT: E 52 THR cc_start: 0.8963 (t) cc_final: 0.8716 (m) REVERT: E 62 LYS cc_start: 0.8404 (mmtp) cc_final: 0.8065 (mmmt) REVERT: E 63 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8847 (m) REVERT: E 206 LYS cc_start: 0.7978 (mmpt) cc_final: 0.7667 (mmmt) REVERT: E 269 ASP cc_start: 0.7762 (m-30) cc_final: 0.7549 (m-30) REVERT: E 291 LYS cc_start: 0.8364 (mmmt) cc_final: 0.8136 (mttp) REVERT: E 292 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7317 (tm130) REVERT: E 325 MET cc_start: 0.9327 (ttt) cc_final: 0.8994 (ttt) REVERT: E 412 ARG cc_start: 0.8043 (ptt180) cc_final: 0.7698 (ptt180) REVERT: E 456 PHE cc_start: 0.8728 (t80) cc_final: 0.8405 (t80) REVERT: E 459 TYR cc_start: 0.7919 (t80) cc_final: 0.7507 (t80) REVERT: F 63 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8820 (m) REVERT: F 292 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7322 (tm130) REVERT: F 325 MET cc_start: 0.9318 (ttt) cc_final: 0.9012 (ttt) REVERT: F 459 TYR cc_start: 0.7898 (t80) cc_final: 0.7660 (t80) REVERT: G 52 THR cc_start: 0.8925 (t) cc_final: 0.8718 (m) REVERT: G 62 LYS cc_start: 0.8439 (mmtp) cc_final: 0.8084 (mmmt) REVERT: G 63 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8825 (m) REVERT: G 292 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7325 (tm130) REVERT: G 325 MET cc_start: 0.9334 (ttt) cc_final: 0.9040 (ttt) REVERT: G 412 ARG cc_start: 0.7824 (ptt180) cc_final: 0.7362 (ptt180) REVERT: G 456 PHE cc_start: 0.8765 (t80) cc_final: 0.8499 (t80) REVERT: G 459 TYR cc_start: 0.8008 (t80) cc_final: 0.7562 (t80) REVERT: G 470 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7719 (m-30) REVERT: H 52 THR cc_start: 0.8963 (t) cc_final: 0.8683 (m) REVERT: H 62 LYS cc_start: 0.8423 (mmtp) cc_final: 0.8155 (mmmt) REVERT: H 63 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8833 (m) REVERT: H 162 ASP cc_start: 0.7661 (m-30) cc_final: 0.7452 (m-30) REVERT: H 217 GLU cc_start: 0.6237 (mp0) cc_final: 0.5718 (pm20) REVERT: H 269 ASP cc_start: 0.7792 (m-30) cc_final: 0.7556 (m-30) REVERT: H 292 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7326 (tm130) REVERT: H 325 MET cc_start: 0.9312 (ttt) cc_final: 0.8977 (ttt) REVERT: H 420 MET cc_start: 0.8012 (mtm) cc_final: 0.7743 (mtp) REVERT: H 459 TYR cc_start: 0.7827 (t80) cc_final: 0.7547 (t80) outliers start: 114 outliers final: 63 residues processed: 738 average time/residue: 2.2754 time to fit residues: 2017.7325 Evaluate side-chains 595 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 521 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 438 LYS Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 470 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 438 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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: 69.1304 > 50: distance: 28 - 41: 3.284 distance: 67 - 89: 27.789 distance: 89 - 90: 48.020 distance: 89 - 97: 15.869 distance: 90 - 91: 31.088 distance: 90 - 93: 17.517 distance: 90 - 98: 22.501 distance: 91 - 92: 23.950 distance: 91 - 108: 42.350 distance: 93 - 94: 3.066 distance: 93 - 95: 24.780 distance: 93 - 99: 37.853 distance: 94 - 96: 43.957 distance: 94 - 100: 47.736 distance: 94 - 101: 24.656 distance: 95 - 102: 23.774 distance: 95 - 103: 18.155 distance: 95 - 104: 22.972 distance: 96 - 105: 8.636 distance: 96 - 106: 42.037 distance: 96 - 107: 40.777 distance: 108 - 117: 40.033 distance: 109 - 110: 6.344 distance: 109 - 118: 39.691 distance: 110 - 111: 35.842 distance: 110 - 123: 4.494 distance: 112 - 113: 20.951 distance: 112 - 119: 40.005 distance: 113 - 114: 42.137 distance: 113 - 121: 6.239 distance: 113 - 122: 20.145 distance: 114 - 116: 4.074 distance: 123 - 124: 9.194 distance: 123 - 131: 40.381 distance: 124 - 125: 31.076 distance: 124 - 127: 47.635 distance: 124 - 132: 29.568 distance: 125 - 142: 27.102 distance: 127 - 128: 44.049 distance: 127 - 133: 40.050 distance: 127 - 134: 46.842 distance: 128 - 129: 55.843 distance: 129 - 136: 23.312 distance: 129 - 137: 12.453 distance: 129 - 138: 13.237 distance: 130 - 139: 12.443 distance: 130 - 140: 7.298 distance: 130 - 141: 16.576 distance: 142 - 143: 14.240 distance: 142 - 149: 14.282 distance: 143 - 144: 49.761 distance: 143 - 146: 41.183 distance: 143 - 150: 41.493 distance: 144 - 145: 30.792 distance: 144 - 158: 40.822 distance: 146 - 147: 39.354 distance: 146 - 148: 34.891 distance: 147 - 152: 36.798 distance: 147 - 153: 40.814 distance: 147 - 154: 25.818 distance: 148 - 156: 13.823 distance: 160 - 174: 56.881 distance: 162 - 163: 43.597 distance: 162 - 164: 40.289 distance: 163 - 168: 45.522 distance: 163 - 169: 40.221 distance: 163 - 170: 19.827 distance: 164 - 173: 18.566 distance: 174 - 179: 39.463 distance: 175 - 178: 47.544 distance: 175 - 180: 43.065 distance: 178 - 181: 13.738 distance: 178 - 183: 42.695 distance: 184 - 185: 47.843 distance: 185 - 186: 29.637 distance: 185 - 188: 24.950 distance: 185 - 191: 12.151 distance: 186 - 198: 54.373 distance: 188 - 189: 59.188 distance: 188 - 192: 21.318 distance: 188 - 193: 16.990 distance: 189 - 190: 39.147 distance: 190 - 196: 11.449 distance: 190 - 197: 39.979 distance: 198 - 199: 4.680 distance: 198 - 203: 4.618 distance: 199 - 200: 52.083 distance: 199 - 204: 43.147 distance: 200 - 201: 35.421 distance: 200 - 208: 7.465 distance: 202 - 205: 39.131 distance: 202 - 206: 56.094 distance: 202 - 207: 19.619 distance: 210 - 211: 39.704 distance: 215 - 222: 4.624 distance: 216 - 217: 55.927 distance: 216 - 219: 7.775 distance: 216 - 223: 39.688 distance: 217 - 218: 59.648 distance: 217 - 231: 33.038 distance: 219 - 220: 31.075 distance: 219 - 221: 35.904 distance: 219 - 224: 4.918 distance: 220 - 225: 5.999 distance: 220 - 226: 23.072 distance: 220 - 227: 32.612 distance: 221 - 228: 6.702 distance: 221 - 229: 21.518 distance: 221 - 230: 21.062 distance: 234 - 261: 3.313