Starting phenix.real_space_refine on Sat May 2 17:26:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jhn_36280/05_2026/8jhn_36280.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jhn_36280/05_2026/8jhn_36280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jhn_36280/05_2026/8jhn_36280.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jhn_36280/05_2026/8jhn_36280.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jhn_36280/05_2026/8jhn_36280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jhn_36280/05_2026/8jhn_36280.map" } resolution = 3.75 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 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= 0.001 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 4911 2.51 5 N 1368 2.21 5 O 1449 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7773 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1489 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 4, 'TRANS': 201} Chain breaks: 2 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 7, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "B" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2375 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 282 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 12, 'GLN:plan1': 3, 'ARG:plan': 8, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 133 Chain: "D" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 1869 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 277} Chain breaks: 2 Unresolved non-hydrogen bonds: 526 Unresolved non-hydrogen angles: 669 Unresolved non-hydrogen dihedrals: 444 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'ASP:plan': 10, 'HIS:plan': 2, 'PHE:plan': 20, 'GLU:plan': 5, 'ARG:plan': 10, 'ASN:plan1': 6, 'TRP:plan': 2, 'GLN:plan1': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 289 Chain: "G" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 376 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1655 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'UR9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.92, per 1000 atoms: 0.25 Number of scatterers: 7773 At special positions: 0 Unit cell: (86.922, 117.652, 132.578, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 1449 8.00 N 1368 7.00 C 4911 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS D 18 " - pdb=" SG CYS D 183 " distance=2.04 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 266 " distance=2.04 Simple disulfide: pdb=" SG CYS D 100 " - pdb=" SG CYS D 177 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 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: 0.65 Conformation dependent library (CDL) restraints added in 472.6 milliseconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2092 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 15 sheets defined 37.1% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 removed outlier: 3.523A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.520A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 212 through 217 removed outlier: 3.503A pdb=" N PHE A 216 " --> pdb=" O ILE A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 removed outlier: 3.625A pdb=" N ASN A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 261 removed outlier: 4.168A pdb=" N ILE A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.532A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'D' and resid 24 through 52 removed outlier: 3.669A pdb=" N LYS D 28 " --> pdb=" O ASP D 24 " (cutoff:3.500A) Proline residue: D 31 - end of helix removed outlier: 4.063A pdb=" N LEU D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 89 Proline residue: D 81 - end of helix Processing helix chain 'D' and resid 96 through 131 removed outlier: 3.571A pdb=" N HIS D 131 " --> pdb=" O PHE D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 160 Processing helix chain 'D' and resid 160 through 165 removed outlier: 3.753A pdb=" N LYS D 164 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS D 165 " --> pdb=" O HIS D 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 160 through 165' Processing helix chain 'D' and resid 187 through 218 removed outlier: 3.574A pdb=" N ALA D 191 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Proline residue: D 200 - end of helix Processing helix chain 'D' and resid 219 through 222 removed outlier: 3.953A pdb=" N ARG D 222 " --> pdb=" O GLN D 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 219 through 222' Processing helix chain 'D' and resid 223 through 262 removed outlier: 4.178A pdb=" N ALA D 237 " --> pdb=" O ILE D 233 " (cutoff:3.500A) Proline residue: D 246 - end of helix Processing helix chain 'D' and resid 268 through 289 removed outlier: 4.300A pdb=" N VAL D 272 " --> pdb=" O VAL D 268 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE D 282 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR D 283 " --> pdb=" O THR D 279 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 295 removed outlier: 3.658A pdb=" N TYR D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 305 Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.737A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.510A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.732A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 56 removed outlier: 3.841A pdb=" N GLY H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 220 through 224 removed outlier: 4.149A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 192 removed outlier: 9.853A pdb=" N ALA A 221 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.704A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.058A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.748A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.800A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.780A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.947A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.877A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 12 through 13 Processing sheet with id=AB1, first strand: chain 'D' and resid 169 through 171 Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.748A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR H 118 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.748A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR H 118 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 140 through 142 removed outlier: 3.578A pdb=" N VAL H 155 " --> pdb=" O ILE H 216 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE H 157 " --> pdb=" O LEU H 214 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS H 159 " --> pdb=" O PHE H 212 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE H 212 " --> pdb=" O CYS H 159 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR H 213 " --> pdb=" O SER H 206 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 194 through 195 removed outlier: 3.626A pdb=" N TYR H 190 " --> pdb=" O ASN H 194 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY H 225 " --> pdb=" O LEU H 245 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1146 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: 1.17 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1280 1.31 - 1.44: 2223 1.44 - 1.57: 4372 1.57 - 1.69: 0 1.69 - 1.82: 59 Bond restraints: 7934 Sorted by residual: bond pdb=" C ALA D 174 " pdb=" N ASN D 175 " ideal model delta sigma weight residual 1.329 1.269 0.060 1.38e-02 5.25e+03 1.89e+01 bond pdb=" C LEU D 280 " pdb=" O LEU D 280 " ideal model delta sigma weight residual 1.236 1.189 0.046 1.32e-02 5.74e+03 1.23e+01 bond pdb=" N SER D 261 " pdb=" CA SER D 261 " ideal model delta sigma weight residual 1.459 1.490 -0.031 9.10e-03 1.21e+04 1.13e+01 bond pdb=" N THR D 263 " pdb=" CA THR D 263 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.22e-02 6.72e+03 9.07e+00 bond pdb=" N GLN D 170 " pdb=" CA GLN D 170 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.27e-02 6.20e+03 8.40e+00 ... (remaining 7929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 10743 2.75 - 5.51: 82 5.51 - 8.26: 19 8.26 - 11.02: 2 11.02 - 13.77: 1 Bond angle restraints: 10847 Sorted by residual: angle pdb=" C ILE D 169 " pdb=" N GLN D 170 " pdb=" CA GLN D 170 " ideal model delta sigma weight residual 122.84 114.69 8.15 1.30e+00 5.92e-01 3.93e+01 angle pdb=" O ILE D 169 " pdb=" C ILE D 169 " pdb=" N GLN D 170 " ideal model delta sigma weight residual 123.18 116.56 6.62 1.08e+00 8.57e-01 3.75e+01 angle pdb=" N ASN D 17 " pdb=" CA ASN D 17 " pdb=" C ASN D 17 " ideal model delta sigma weight residual 110.30 101.18 9.12 1.50e+00 4.44e-01 3.70e+01 angle pdb=" N PHE D 197 " pdb=" CA PHE D 197 " pdb=" C PHE D 197 " ideal model delta sigma weight residual 113.55 106.57 6.98 1.26e+00 6.30e-01 3.07e+01 angle pdb=" N LEU D 280 " pdb=" CA LEU D 280 " pdb=" C LEU D 280 " ideal model delta sigma weight residual 112.89 106.04 6.85 1.24e+00 6.50e-01 3.05e+01 ... (remaining 10842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 4216 16.70 - 33.40: 305 33.40 - 50.10: 69 50.10 - 66.80: 9 66.80 - 83.50: 6 Dihedral angle restraints: 4605 sinusoidal: 1371 harmonic: 3234 Sorted by residual: dihedral pdb=" CB CYS D 19 " pdb=" SG CYS D 19 " pdb=" SG CYS D 266 " pdb=" CB CYS D 266 " ideal model delta sinusoidal sigma weight residual 93.00 176.50 -83.50 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" CB CYS H 159 " pdb=" SG CYS H 159 " pdb=" SG CYS H 229 " pdb=" CB CYS H 229 " ideal model delta sinusoidal sigma weight residual 93.00 139.53 -46.53 1 1.00e+01 1.00e-02 3.00e+01 dihedral pdb=" CA ALA D 174 " pdb=" C ALA D 174 " pdb=" N ASN D 175 " pdb=" CA ASN D 175 " ideal model delta harmonic sigma weight residual 180.00 156.74 23.26 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 4602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 862 0.037 - 0.074: 294 0.074 - 0.111: 89 0.111 - 0.148: 24 0.148 - 0.185: 6 Chirality restraints: 1275 Sorted by residual: chirality pdb=" CB VAL A 202 " pdb=" CA VAL A 202 " pdb=" CG1 VAL A 202 " pdb=" CG2 VAL A 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.56e-01 chirality pdb=" CA PHE D 25 " pdb=" N PHE D 25 " pdb=" C PHE D 25 " pdb=" CB PHE D 25 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.36e-01 chirality pdb=" CA LEU D 258 " pdb=" N LEU D 258 " pdb=" C LEU D 258 " pdb=" CB LEU D 258 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.93e-01 ... (remaining 1272 not shown) Planarity restraints: 1409 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 280 " -0.020 2.00e-02 2.50e+03 4.17e-02 1.74e+01 pdb=" C LEU D 280 " 0.072 2.00e-02 2.50e+03 pdb=" O LEU D 280 " -0.027 2.00e-02 2.50e+03 pdb=" N SER D 281 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 169 " 0.016 2.00e-02 2.50e+03 2.97e-02 8.80e+00 pdb=" C ILE D 169 " -0.051 2.00e-02 2.50e+03 pdb=" O ILE D 169 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN D 170 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 260 " -0.013 2.00e-02 2.50e+03 2.71e-02 7.33e+00 pdb=" C THR D 260 " 0.047 2.00e-02 2.50e+03 pdb=" O THR D 260 " -0.018 2.00e-02 2.50e+03 pdb=" N SER D 261 " -0.016 2.00e-02 2.50e+03 ... (remaining 1406 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 583 2.74 - 3.28: 7783 3.28 - 3.82: 12523 3.82 - 4.36: 13310 4.36 - 4.90: 24667 Nonbonded interactions: 58866 Sorted by model distance: nonbonded pdb=" NE2 GLN A 333 " pdb=" OD2 ASP A 337 " model vdw 2.198 3.120 nonbonded pdb=" O LEU D 66 " pdb=" OH TYR D 294 " model vdw 2.236 3.040 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.240 3.040 nonbonded pdb=" O TYR D 284 " pdb=" OG SER D 287 " model vdw 2.262 3.040 nonbonded pdb=" OG1 THR H 91 " pdb=" O LEU H 117 " model vdw 2.269 3.040 ... (remaining 58861 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.810 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7939 Z= 0.218 Angle : 0.669 13.771 10857 Z= 0.410 Chirality : 0.044 0.185 1275 Planarity : 0.004 0.045 1409 Dihedral : 12.795 75.311 2498 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.60 % Allowed : 0.75 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.27), residues: 1098 helix: 2.06 (0.29), residues: 360 sheet: -0.46 (0.32), residues: 276 loop : -0.29 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 160 TYR 0.010 0.001 TYR H 190 PHE 0.010 0.001 PHE B 151 TRP 0.014 0.001 TRP B 297 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 7934) covalent geometry : angle 0.66863 (10847) SS BOND : bond 0.00341 ( 5) SS BOND : angle 1.19773 ( 10) hydrogen bonds : bond 0.19755 ( 405) hydrogen bonds : angle 7.08732 ( 1146) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 133 time to evaluate : 0.300 Fit side-chains REVERT: A 53 MET cc_start: 0.5566 (mpp) cc_final: 0.3329 (mtm) REVERT: A 211 LYS cc_start: 0.7759 (mmtt) cc_final: 0.7376 (mmtp) REVERT: A 333 GLN cc_start: 0.7929 (tm-30) cc_final: 0.7670 (tm-30) REVERT: H 246 GLU cc_start: 0.8276 (mp0) cc_final: 0.7519 (pm20) outliers start: 4 outliers final: 0 residues processed: 137 average time/residue: 0.0870 time to fit residues: 16.1741 Evaluate side-chains 108 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 17 GLN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.137873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.113567 restraints weight = 14904.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.114275 restraints weight = 12339.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.115809 restraints weight = 10414.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.116054 restraints weight = 7552.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.116307 restraints weight = 7033.889| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7939 Z= 0.167 Angle : 0.559 8.644 10857 Z= 0.300 Chirality : 0.043 0.147 1275 Planarity : 0.004 0.046 1409 Dihedral : 4.158 47.906 1184 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.19 % Allowed : 9.09 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.27), residues: 1098 helix: 2.50 (0.28), residues: 367 sheet: -0.54 (0.30), residues: 292 loop : -0.13 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 98 TYR 0.016 0.001 TYR H 190 PHE 0.014 0.001 PHE B 151 TRP 0.020 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 7934) covalent geometry : angle 0.55817 (10847) SS BOND : bond 0.00420 ( 5) SS BOND : angle 0.93474 ( 10) hydrogen bonds : bond 0.03905 ( 405) hydrogen bonds : angle 4.97166 ( 1146) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.273 Fit side-chains REVERT: A 211 LYS cc_start: 0.7949 (mmtt) cc_final: 0.7452 (mmtp) REVERT: A 295 ASN cc_start: 0.8284 (t0) cc_final: 0.7875 (t0) REVERT: A 319 ILE cc_start: 0.9077 (mt) cc_final: 0.8820 (mt) REVERT: A 322 HIS cc_start: 0.6857 (m90) cc_final: 0.6643 (m90) REVERT: A 333 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7630 (tm-30) REVERT: A 337 ASP cc_start: 0.8645 (m-30) cc_final: 0.7710 (m-30) REVERT: H 98 ARG cc_start: 0.8758 (ptm-80) cc_final: 0.8302 (ptm160) outliers start: 8 outliers final: 6 residues processed: 123 average time/residue: 0.0853 time to fit residues: 14.3347 Evaluate side-chains 106 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.8357 > 50: distance: 42 - 138: 22.137 distance: 63 - 72: 11.817 distance: 72 - 73: 33.118 distance: 73 - 74: 30.314 distance: 73 - 76: 26.465 distance: 74 - 75: 48.098 distance: 74 - 80: 24.843 distance: 76 - 77: 13.983 distance: 77 - 78: 31.880 distance: 77 - 79: 28.883 distance: 80 - 81: 3.146 distance: 81 - 82: 48.315 distance: 81 - 84: 18.262 distance: 82 - 83: 14.688 distance: 82 - 88: 28.789 distance: 84 - 85: 22.016 distance: 85 - 86: 16.320 distance: 85 - 87: 8.428 distance: 88 - 89: 15.010 distance: 89 - 90: 12.359 distance: 89 - 92: 17.977 distance: 90 - 91: 23.908 distance: 90 - 96: 13.001 distance: 92 - 93: 15.303 distance: 93 - 94: 9.700 distance: 93 - 95: 22.197 distance: 96 - 97: 12.508 distance: 97 - 98: 9.025 distance: 97 - 100: 5.902 distance: 98 - 99: 5.935 distance: 98 - 104: 7.777 distance: 100 - 101: 18.284 distance: 101 - 102: 8.597 distance: 101 - 103: 26.413 distance: 104 - 105: 11.494 distance: 105 - 106: 4.624 distance: 105 - 108: 11.633 distance: 106 - 107: 5.037 distance: 106 - 113: 19.561 distance: 108 - 109: 15.254 distance: 109 - 110: 20.042 distance: 110 - 111: 10.139 distance: 110 - 112: 31.653 distance: 113 - 114: 5.476 distance: 114 - 115: 3.394 distance: 114 - 117: 8.032 distance: 115 - 116: 11.294 distance: 115 - 121: 7.337 distance: 117 - 118: 9.501 distance: 117 - 119: 10.025 distance: 118 - 120: 15.577 distance: 121 - 122: 6.130 distance: 122 - 123: 7.878 distance: 122 - 125: 5.484 distance: 123 - 124: 22.320 distance: 123 - 128: 16.418 distance: 125 - 126: 16.320 distance: 125 - 127: 24.768 distance: 128 - 129: 10.537 distance: 128 - 167: 22.882 distance: 129 - 130: 22.877 distance: 129 - 132: 31.315 distance: 130 - 131: 24.824 distance: 130 - 135: 13.740 distance: 131 - 164: 30.326 distance: 132 - 133: 38.343 distance: 132 - 134: 31.264 distance: 135 - 136: 10.618 distance: 136 - 137: 9.938 distance: 136 - 139: 18.075 distance: 137 - 138: 22.461 distance: 137 - 141: 3.146 distance: 139 - 140: 12.904 distance: 141 - 142: 9.113 distance: 142 - 143: 8.694 distance: 142 - 145: 10.468 distance: 143 - 144: 10.989 distance: 143 - 146: 4.739