Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 4 20:20:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6s_35205/07_2023/8i6s_35205_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6s_35205/07_2023/8i6s_35205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6s_35205/07_2023/8i6s_35205.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6s_35205/07_2023/8i6s_35205.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6s_35205/07_2023/8i6s_35205_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6s_35205/07_2023/8i6s_35205_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.032 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 6 5.49 5 Mg 2 5.21 5 S 20 5.16 5 C 5581 2.51 5 N 1432 2.21 5 O 1600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 131": "OE1" <-> "OE2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 295": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 8641 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2261 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 288} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 20, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "B" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1680 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 22} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2316 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 12, 'TRANS': 290} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 20} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1679 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 22} Unresolved non-hydrogen planarities: 45 Chain: "E" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 641 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 75} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.72, per 1000 atoms: 0.55 Number of scatterers: 8641 At special positions: 0 Unit cell: (66.066, 78.936, 179.322, 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 20 16.00 P 6 15.00 Mg 2 11.99 O 1600 8.00 N 1432 7.00 C 5581 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 1.4 seconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2050 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 5 sheets defined 51.0% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 37 through 53 Processing helix chain 'A' and resid 56 through 68 removed outlier: 3.540A pdb=" N VAL A 65 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 80 removed outlier: 3.953A pdb=" N MET A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A 77 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 118 removed outlier: 3.730A pdb=" N GLU A 114 " --> pdb=" O GLN A 110 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 141 Processing helix chain 'A' and resid 171 through 177 removed outlier: 3.715A pdb=" N ARG A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 231 removed outlier: 3.541A pdb=" N ILE A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 231 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 243 removed outlier: 3.794A pdb=" N GLU A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 292 removed outlier: 3.547A pdb=" N ARG A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Proline residue: A 254 - end of helix removed outlier: 3.651A pdb=" N TYR A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR A 262 " --> pdb=" O MET A 258 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY A 283 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER A 284 " --> pdb=" O TRP A 280 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL A 286 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ASN A 287 " --> pdb=" O GLY A 283 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 331 removed outlier: 3.508A pdb=" N THR A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 48 Processing helix chain 'B' and resid 71 through 79 Proline residue: B 75 - end of helix Processing helix chain 'B' and resid 96 through 102 removed outlier: 3.708A pdb=" N ILE B 100 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 124 removed outlier: 4.034A pdb=" N ALA B 115 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL B 118 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA B 121 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 122 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU B 123 " --> pdb=" O SER B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 140 through 152 removed outlier: 4.120A pdb=" N GLN B 144 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 185 removed outlier: 4.690A pdb=" N GLU B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU B 181 " --> pdb=" O MET B 177 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 201 No H-bonds generated for 'chain 'B' and resid 199 through 201' Processing helix chain 'C' and resid 34 through 53 Processing helix chain 'C' and resid 56 through 68 removed outlier: 3.632A pdb=" N PHE C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS C 63 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 65 " --> pdb=" O PHE C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 83 removed outlier: 3.833A pdb=" N MET C 74 " --> pdb=" O LEU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 106 through 118 removed outlier: 3.565A pdb=" N ASP C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU C 117 " --> pdb=" O ARG C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 137 removed outlier: 3.912A pdb=" N LEU C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 178 removed outlier: 3.961A pdb=" N LEU C 174 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG C 175 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLN C 176 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN C 177 " --> pdb=" O LEU C 174 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 178 " --> pdb=" O ARG C 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 171 through 178' Processing helix chain 'C' and resid 192 through 195 No H-bonds generated for 'chain 'C' and resid 192 through 195' Processing helix chain 'C' and resid 197 through 200 No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 203 through 232 removed outlier: 3.536A pdb=" N ILE C 213 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL C 222 " --> pdb=" O THR C 218 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG C 228 " --> pdb=" O GLY C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 242 removed outlier: 3.591A pdb=" N ILE C 238 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU C 239 " --> pdb=" O ASN C 236 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL C 240 " --> pdb=" O GLU C 237 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C 242 " --> pdb=" O GLU C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 280 Proline residue: C 254 - end of helix removed outlier: 3.684A pdb=" N TYR C 257 " --> pdb=" O ARG C 253 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR C 262 " --> pdb=" O MET C 258 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 291 Processing helix chain 'C' and resid 304 through 331 removed outlier: 3.869A pdb=" N ALA C 326 " --> pdb=" O TRP C 322 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG C 327 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N HIS C 328 " --> pdb=" O ALA C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 49 removed outlier: 3.661A pdb=" N ILE D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 79 Proline residue: D 75 - end of helix Processing helix chain 'D' and resid 97 through 107 Proline residue: D 103 - end of helix removed outlier: 4.062A pdb=" N ILE D 106 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 121 removed outlier: 4.595A pdb=" N ALA D 115 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS D 116 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG D 117 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA D 119 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER D 120 " --> pdb=" O ARG D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 152 Processing helix chain 'D' and resid 170 through 182 removed outlier: 3.957A pdb=" N SER D 174 " --> pdb=" O PRO D 170 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU D 175 " --> pdb=" O ARG D 171 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU D 181 " --> pdb=" O MET D 177 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP D 182 " --> pdb=" O GLY D 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 115 removed outlier: 4.263A pdb=" N ALA E 98 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN E 115 " --> pdb=" O ARG E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 162 removed outlier: 3.507A pdb=" N ARG E 148 " --> pdb=" O ILE E 144 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU E 149 " --> pdb=" O ASN E 145 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU E 150 " --> pdb=" O LYS E 146 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR E 158 " --> pdb=" O SER E 154 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN E 161 " --> pdb=" O GLU E 157 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 124 through 127 Processing sheet with id= B, first strand: chain 'B' and resid 2 through 4 removed outlier: 3.773A pdb=" N PHE B 4 " --> pdb=" O PHE B 23 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 59 through 61 removed outlier: 4.468A pdb=" N LEU B 59 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU B 61 " --> pdb=" O GLN B 64 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN B 64 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.610A pdb=" N VAL C 161 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU C 98 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE C 159 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 158 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C 128 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN C 126 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 190 through 193 removed outlier: 3.882A pdb=" N VAL D 33 " --> pdb=" O ILE D 192 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU D 208 " --> pdb=" O THR D 34 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 924 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: 2.05 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2048 1.33 - 1.46: 1723 1.46 - 1.58: 4967 1.58 - 1.70: 10 1.70 - 1.83: 38 Bond restraints: 8786 Sorted by residual: bond pdb=" C6 ATP D 301 " pdb=" N6 ATP D 301 " ideal model delta sigma weight residual 1.337 1.449 -0.112 1.10e-02 8.26e+03 1.04e+02 bond pdb=" C6 ATP B 302 " pdb=" N6 ATP B 302 " ideal model delta sigma weight residual 1.337 1.449 -0.112 1.10e-02 8.26e+03 1.03e+02 bond pdb=" C5 ATP B 302 " pdb=" N7 ATP B 302 " ideal model delta sigma weight residual 1.387 1.469 -0.082 1.00e-02 1.00e+04 6.69e+01 bond pdb=" C5 ATP D 301 " pdb=" N7 ATP D 301 " ideal model delta sigma weight residual 1.387 1.468 -0.081 1.00e-02 1.00e+04 6.57e+01 bond pdb=" O5' ATP D 301 " pdb=" PA ATP D 301 " ideal model delta sigma weight residual 1.579 1.650 -0.071 1.10e-02 8.26e+03 4.14e+01 ... (remaining 8781 not shown) Histogram of bond angle deviations from ideal: 97.81 - 105.50: 182 105.50 - 113.18: 4802 113.18 - 120.87: 4183 120.87 - 128.56: 2637 128.56 - 136.24: 82 Bond angle restraints: 11886 Sorted by residual: angle pdb=" PB ATP B 302 " pdb=" O3B ATP B 302 " pdb=" PG ATP B 302 " ideal model delta sigma weight residual 139.87 116.52 23.35 1.00e+00 1.00e+00 5.45e+02 angle pdb=" PB ATP D 301 " pdb=" O3B ATP D 301 " pdb=" PG ATP D 301 " ideal model delta sigma weight residual 139.87 125.37 14.50 1.00e+00 1.00e+00 2.10e+02 angle pdb=" PA ATP B 302 " pdb=" O3A ATP B 302 " pdb=" PB ATP B 302 " ideal model delta sigma weight residual 136.83 122.76 14.07 1.00e+00 1.00e+00 1.98e+02 angle pdb=" O3A ATP B 302 " pdb=" PB ATP B 302 " pdb=" O3B ATP B 302 " ideal model delta sigma weight residual 101.57 116.72 -15.15 1.54e+00 4.24e-01 9.73e+01 angle pdb=" PA ATP D 301 " pdb=" O3A ATP D 301 " pdb=" PB ATP D 301 " ideal model delta sigma weight residual 136.83 127.43 9.40 1.00e+00 1.00e+00 8.84e+01 ... (remaining 11881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4623 17.97 - 35.95: 547 35.95 - 53.92: 108 53.92 - 71.89: 20 71.89 - 89.86: 6 Dihedral angle restraints: 5304 sinusoidal: 2116 harmonic: 3188 Sorted by residual: dihedral pdb=" CA VAL A 192 " pdb=" C VAL A 192 " pdb=" N TRP A 193 " pdb=" CA TRP A 193 " ideal model delta harmonic sigma weight residual 180.00 137.38 42.62 0 5.00e+00 4.00e-02 7.27e+01 dihedral pdb=" CA ASP C 190 " pdb=" C ASP C 190 " pdb=" N LEU C 191 " pdb=" CA LEU C 191 " ideal model delta harmonic sigma weight residual -180.00 -157.62 -22.38 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LEU A 229 " pdb=" C LEU A 229 " pdb=" N HIS A 230 " pdb=" CA HIS A 230 " ideal model delta harmonic sigma weight residual 180.00 157.90 22.10 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 5301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1133 0.073 - 0.146: 224 0.146 - 0.219: 46 0.219 - 0.292: 5 0.292 - 0.365: 3 Chirality restraints: 1411 Sorted by residual: chirality pdb=" CB ILE B 215 " pdb=" CA ILE B 215 " pdb=" CG1 ILE B 215 " pdb=" CG2 ILE B 215 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB ILE D 2 " pdb=" CA ILE D 2 " pdb=" CG1 ILE D 2 " pdb=" CG2 ILE D 2 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CB VAL B 125 " pdb=" CA VAL B 125 " pdb=" CG1 VAL B 125 " pdb=" CG2 VAL B 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 1408 not shown) Planarity restraints: 1476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 195 " -0.045 2.00e-02 2.50e+03 6.17e-02 5.71e+01 pdb=" CG HIS B 195 " 0.107 2.00e-02 2.50e+03 pdb=" ND1 HIS B 195 " -0.056 2.00e-02 2.50e+03 pdb=" CD2 HIS B 195 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS B 195 " 0.050 2.00e-02 2.50e+03 pdb=" NE2 HIS B 195 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 192 " -0.025 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C VAL A 192 " 0.085 2.00e-02 2.50e+03 pdb=" O VAL A 192 " -0.032 2.00e-02 2.50e+03 pdb=" N TRP A 193 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 280 " -0.013 2.00e-02 2.50e+03 1.55e-02 6.01e+00 pdb=" CG TRP C 280 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP C 280 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP C 280 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 280 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 280 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 280 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 280 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 280 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 280 " 0.001 2.00e-02 2.50e+03 ... (remaining 1473 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 86 2.64 - 3.20: 7084 3.20 - 3.77: 13855 3.77 - 4.33: 17647 4.33 - 4.90: 27274 Nonbonded interactions: 65946 Sorted by model distance: nonbonded pdb=" OG1 THR B 140 " pdb="MG MG B 301 " model vdw 2.073 2.170 nonbonded pdb="MG MG B 301 " pdb=" O3A ATP D 301 " model vdw 2.077 2.170 nonbonded pdb=" O1A ATP B 302 " pdb="MG MG B 303 " model vdw 2.133 2.170 nonbonded pdb="MG MG B 301 " pdb=" O2B ATP D 301 " model vdw 2.135 2.170 nonbonded pdb=" O1B ATP B 302 " pdb="MG MG B 303 " model vdw 2.253 2.170 ... (remaining 65941 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 'C' and (resid 35 through 88 or (resid 89 and (name N or name CA or name \ C or name O or name CB )) or resid 90 or (resid 91 through 95 and (name N or nam \ e CA or name C or name O or name CB )) or resid 96 through 122 or (resid 123 and \ (name N or name CA or name C or name O or name CB )) or resid 124 through 164 o \ r (resid 165 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 66 or (resid 167 through 169 and (name N or name CA or name C or name O or name \ CB )) or resid 170 or (resid 171 and (name N or name CA or name C or name O or n \ ame CB )) or resid 172 through 194 or (resid 195 and (name N or name CA or name \ C or name O or name CB )) or resid 196 or (resid 197 through 199 and (name N or \ name CA or name C or name O or name CB )) or resid 200 through 335)) } ncs_group { reference = (chain 'B' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ )) or resid 12 through 222)) selection = (chain 'D' and resid 1 through 222) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 26.310 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 24.770 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6010 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 : 0.006 0.112 8786 Z= 0.419 Angle : 1.394 23.352 11886 Z= 0.763 Chirality : 0.063 0.365 1411 Planarity : 0.007 0.062 1476 Dihedral : 15.969 89.863 3254 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.13 % Favored : 95.70 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -5.18 (0.17), residues: 1115 helix: -4.23 (0.09), residues: 575 sheet: -0.91 (0.68), residues: 55 loop : -2.52 (0.22), residues: 485 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 1.005 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 9 residues processed: 126 average time/residue: 0.1624 time to fit residues: 30.4786 Evaluate side-chains 85 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 1.034 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 9 average time/residue: 0.1428 time to fit residues: 3.2297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 0.0170 chunk 100 optimal weight: 0.8980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 230 HIS ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6060 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 8786 Z= 0.155 Angle : 0.627 7.312 11886 Z= 0.315 Chirality : 0.040 0.150 1411 Planarity : 0.004 0.035 1476 Dihedral : 5.736 49.647 1151 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.23 % Favored : 96.59 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.21), residues: 1115 helix: -1.64 (0.19), residues: 569 sheet: -0.82 (0.71), residues: 53 loop : -2.01 (0.24), residues: 493 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 1.043 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 9 residues processed: 109 average time/residue: 0.1666 time to fit residues: 27.4632 Evaluate side-chains 80 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.975 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 9 average time/residue: 0.1395 time to fit residues: 3.2459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/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: 62.142 > 50: distance: 19 - 24: 20.802 distance: 24 - 25: 23.177 distance: 25 - 26: 35.986 distance: 25 - 28: 14.911 distance: 26 - 27: 32.947 distance: 26 - 33: 27.426 distance: 28 - 29: 8.856 distance: 29 - 30: 12.540 distance: 30 - 31: 38.036 distance: 31 - 32: 14.881 distance: 33 - 34: 26.278 distance: 34 - 35: 36.030 distance: 34 - 37: 29.425 distance: 35 - 36: 29.657 distance: 35 - 44: 19.251 distance: 37 - 38: 8.186 distance: 38 - 39: 32.925 distance: 38 - 40: 31.613 distance: 39 - 41: 18.406 distance: 40 - 42: 18.967 distance: 41 - 43: 23.570 distance: 42 - 43: 15.755 distance: 44 - 45: 21.845 distance: 44 - 50: 28.704 distance: 45 - 46: 16.342 distance: 45 - 48: 34.544 distance: 46 - 47: 36.680 distance: 46 - 51: 45.944 distance: 48 - 49: 4.321 distance: 49 - 50: 17.437 distance: 51 - 52: 10.717 distance: 52 - 53: 22.830 distance: 52 - 55: 44.317 distance: 53 - 54: 27.352 distance: 53 - 59: 30.300 distance: 55 - 56: 17.443 distance: 56 - 57: 32.508 distance: 56 - 58: 22.833 distance: 59 - 60: 26.177 distance: 60 - 61: 18.945 distance: 61 - 62: 12.232 distance: 61 - 63: 7.806 distance: 63 - 64: 19.429 distance: 64 - 65: 18.902 distance: 64 - 67: 32.312 distance: 65 - 66: 18.723 distance: 65 - 73: 42.486 distance: 67 - 68: 21.914 distance: 68 - 69: 15.946 distance: 68 - 70: 27.301 distance: 69 - 71: 22.461 distance: 70 - 72: 11.981 distance: 71 - 72: 7.924 distance: 73 - 74: 36.941 distance: 74 - 75: 49.539 distance: 74 - 77: 28.528 distance: 75 - 76: 12.986 distance: 75 - 80: 25.734 distance: 77 - 78: 27.129 distance: 77 - 79: 24.516 distance: 80 - 81: 35.006 distance: 81 - 82: 18.712 distance: 82 - 83: 18.784 distance: 82 - 84: 23.051 distance: 84 - 85: 8.921 distance: 85 - 86: 16.542 distance: 85 - 88: 3.926 distance: 86 - 87: 7.370 distance: 86 - 92: 26.450 distance: 88 - 89: 5.478 distance: 89 - 90: 3.091 distance: 89 - 91: 10.890 distance: 92 - 93: 26.514 distance: 93 - 94: 12.020 distance: 93 - 96: 17.963 distance: 94 - 95: 19.026 distance: 94 - 102: 14.647 distance: 96 - 97: 17.058 distance: 97 - 98: 7.219 distance: 97 - 99: 5.573 distance: 98 - 100: 9.322 distance: 99 - 101: 9.205