Starting phenix.real_space_refine on Sat Aug 23 12:11:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7q_28907/08_2025/8f7q_28907.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7q_28907/08_2025/8f7q_28907.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f7q_28907/08_2025/8f7q_28907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7q_28907/08_2025/8f7q_28907.map" model { file = "/net/cci-nas-00/data/ceres_data/8f7q_28907/08_2025/8f7q_28907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7q_28907/08_2025/8f7q_28907.cif" } resolution = 3.22 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= -0.000 sd= 0.009 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 100 5.16 5 C 7797 2.51 5 N 1949 2.21 5 O 2148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11994 Number of models: 1 Model: "" Number of chains: 11 Chain: "R" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2312 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "P" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 162 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "A" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1816 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2576 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 329} Chain: "C" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 437 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "E" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1788 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "M" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2312 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "Q" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 162 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "F" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Modifications used: {'COO': 1} Link IDs: {'TRANS': 18} Chain: "R" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 3.03, per 1000 atoms: 0.25 Number of scatterers: 11994 At special positions: 0 Unit cell: (111.384, 112.455, 152.082, 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 100 16.00 O 2148 8.00 N 1949 7.00 C 7797 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 142 " - pdb=" SG CYS R 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.04 Simple disulfide: pdb=" SG CYS M 142 " - pdb=" SG CYS M 219 " distance=2.03 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: 0.97 Conformation dependent library (CDL) restraints added in 584.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2802 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 15 sheets defined 49.3% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'R' and resid 66 through 98 Processing helix chain 'R' and resid 103 through 122 Processing helix chain 'R' and resid 122 through 133 removed outlier: 3.743A pdb=" N GLN R 126 " --> pdb=" O THR R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 173 Processing helix chain 'R' and resid 173 through 181 removed outlier: 3.597A pdb=" N LEU R 178 " --> pdb=" O PRO R 174 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 207 removed outlier: 4.080A pdb=" N ILE R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) Proline residue: R 203 - end of helix Processing helix chain 'R' and resid 226 through 264 removed outlier: 3.594A pdb=" N TRP R 230 " --> pdb=" O PRO R 226 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N MET R 245 " --> pdb=" O PHE R 241 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 270 through 308 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 313 through 339 removed outlier: 3.858A pdb=" N ASN R 330 " --> pdb=" O LEU R 326 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER R 331 " --> pdb=" O GLY R 327 " (cutoff:3.500A) Proline residue: R 335 - end of helix Processing helix chain 'R' and resid 342 through 352 Processing helix chain 'P' and resid 12 through 21 removed outlier: 3.677A pdb=" N THR P 16 " --> pdb=" O THR P 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 33 Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.211A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 217 removed outlier: 4.457A pdb=" N GLY A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.795A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.593A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 11 through 24 Processing helix chain 'C' and resid 29 through 45 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.256A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'M' and resid 67 through 98 Processing helix chain 'M' and resid 103 through 122 removed outlier: 3.909A pdb=" N THR M 122 " --> pdb=" O LEU M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 133 Processing helix chain 'M' and resid 138 through 173 removed outlier: 3.619A pdb=" N PHE M 154 " --> pdb=" O TYR M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 181 removed outlier: 3.795A pdb=" N ASP M 179 " --> pdb=" O VAL M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 207 removed outlier: 3.811A pdb=" N ILE M 200 " --> pdb=" O LEU M 196 " (cutoff:3.500A) Proline residue: M 203 - end of helix Processing helix chain 'M' and resid 226 through 264 removed outlier: 3.566A pdb=" N TRP M 230 " --> pdb=" O PRO M 226 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N MET M 245 " --> pdb=" O PHE M 241 " (cutoff:3.500A) Proline residue: M 246 - end of helix removed outlier: 3.652A pdb=" N SER M 263 " --> pdb=" O LEU M 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 308 Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 313 through 340 removed outlier: 3.874A pdb=" N SER M 331 " --> pdb=" O GLY M 327 " (cutoff:3.500A) Proline residue: M 335 - end of helix Processing helix chain 'M' and resid 342 through 352 Processing helix chain 'Q' and resid 12 through 21 removed outlier: 3.761A pdb=" N THR Q 16 " --> pdb=" O THR Q 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 352 Processing sheet with id=AA1, first strand: chain 'R' and resid 208 through 213 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.742A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 268 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.148A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.758A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.611A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.670A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.623A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.456A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.687A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.736A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.736A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.694A pdb=" N GLU E 247 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU E 175 " --> pdb=" O TYR E 191 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N TYR E 191 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP E 177 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 156 through 160 Processing sheet with id=AB6, first strand: chain 'M' and resid 208 through 213 703 hydrogen bonds defined for protein. 2034 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: 2.20 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3659 1.34 - 1.46: 2776 1.46 - 1.58: 5694 1.58 - 1.70: 0 1.70 - 1.82: 149 Bond restraints: 12278 Sorted by residual: bond pdb=" C ASN R 334 " pdb=" N PRO R 335 " ideal model delta sigma weight residual 1.335 1.397 -0.062 1.30e-02 5.92e+03 2.24e+01 bond pdb=" C LEU M 202 " pdb=" N PRO M 203 " ideal model delta sigma weight residual 1.335 1.362 -0.027 1.28e-02 6.10e+03 4.50e+00 bond pdb=" C LEU R 202 " pdb=" N PRO R 203 " ideal model delta sigma weight residual 1.335 1.362 -0.027 1.36e-02 5.41e+03 3.85e+00 bond pdb=" C LEU R 123 " pdb=" N PRO R 124 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.28e-02 6.10e+03 3.49e+00 bond pdb=" C THR R 296 " pdb=" N PRO R 297 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.33e+00 ... (remaining 12273 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 15867 1.81 - 3.62: 695 3.62 - 5.43: 108 5.43 - 7.24: 27 7.24 - 9.05: 6 Bond angle restraints: 16703 Sorted by residual: angle pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta sigma weight residual 125.02 131.81 -6.79 1.76e+00 3.23e-01 1.49e+01 angle pdb=" N LEU R 123 " pdb=" CA LEU R 123 " pdb=" C LEU R 123 " ideal model delta sigma weight residual 109.81 117.47 -7.66 2.21e+00 2.05e-01 1.20e+01 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 124.82 130.67 -5.85 1.78e+00 3.16e-01 1.08e+01 angle pdb=" C GLY E 210 " pdb=" N THR E 211 " pdb=" CA THR E 211 " ideal model delta sigma weight residual 125.66 131.62 -5.96 1.85e+00 2.92e-01 1.04e+01 angle pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 124.82 130.46 -5.64 1.78e+00 3.16e-01 1.00e+01 ... (remaining 16698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.13: 7365 14.13 - 28.27: 321 28.27 - 42.40: 55 42.40 - 56.53: 4 56.53 - 70.67: 3 Dihedral angle restraints: 7748 sinusoidal: 3414 harmonic: 4334 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 158.92 21.08 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 161.19 18.81 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 7745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1709 0.082 - 0.165: 192 0.165 - 0.247: 31 0.247 - 0.330: 10 0.330 - 0.412: 11 Chirality restraints: 1953 Sorted by residual: chirality pdb=" C14 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C15 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" C14 CLR M 405 " pdb=" C13 CLR M 405 " pdb=" C15 CLR M 405 " pdb=" C8 CLR M 405 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" C14 CLR M 402 " pdb=" C13 CLR M 402 " pdb=" C15 CLR M 402 " pdb=" C8 CLR M 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.40 2.00e-01 2.50e+01 3.98e+00 ... (remaining 1950 not shown) Planarity restraints: 2013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL M 336 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.12e+00 pdb=" C VAL M 336 " -0.046 2.00e-02 2.50e+03 pdb=" O VAL M 336 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU M 337 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO B 236 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 219 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C ARG E 219 " -0.033 2.00e-02 2.50e+03 pdb=" O ARG E 219 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU E 220 " 0.011 2.00e-02 2.50e+03 ... (remaining 2010 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2268 2.79 - 3.32: 10934 3.32 - 3.84: 19401 3.84 - 4.37: 21736 4.37 - 4.90: 39457 Nonbonded interactions: 93796 Sorted by model distance: nonbonded pdb=" O ALA M 325 " pdb=" OG1 THR M 329 " model vdw 2.262 3.040 nonbonded pdb=" OG SER E 205 " pdb=" OG1 THR E 216 " model vdw 2.276 3.040 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.314 3.040 nonbonded pdb=" O ILE M 292 " pdb=" OG1 THR M 296 " model vdw 2.360 3.040 nonbonded pdb=" O LYS A 35 " pdb=" OG1 THR A 219 " model vdw 2.360 3.040 ... (remaining 93791 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 'M' selection = chain 'R' } ncs_group { reference = chain 'P' selection = chain 'Q' } 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: 0.700 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.440 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 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 0.063 12281 Z= 0.242 Angle : 0.868 9.050 16709 Z= 0.476 Chirality : 0.065 0.412 1953 Planarity : 0.006 0.050 2013 Dihedral : 8.264 70.668 4937 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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 aren not related in a simple way. whole: 0.89 (0.20), residues: 1462 helix: 1.88 (0.17), residues: 668 sheet: 0.50 (0.30), residues: 283 loop : -1.10 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.028 0.002 TYR R 301 PHE 0.032 0.002 PHE Q 18 TRP 0.027 0.002 TRP E 111 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00439 (12278) covalent geometry : angle 0.86774 (16703) SS BOND : bond 0.00623 ( 3) SS BOND : angle 1.94012 ( 6) hydrogen bonds : bond 0.11550 ( 699) hydrogen bonds : angle 5.75920 ( 2034) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: R 163 MET cc_start: 0.8330 (mtp) cc_final: 0.8119 (mtp) REVERT: E 159 SER cc_start: 0.8060 (t) cc_final: 0.7788 (p) REVERT: E 187 GLN cc_start: 0.8014 (pt0) cc_final: 0.7788 (pt0) REVERT: M 257 MET cc_start: 0.7689 (ttt) cc_final: 0.7365 (ttt) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.1288 time to fit residues: 41.3482 Evaluate side-chains 149 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0970 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 190 ASN B 35 ASN B 75 GLN B 91 HIS B 230 ASN B 237 ASN B 266 HIS E 180 GLN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 ASN M 330 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.178809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.144716 restraints weight = 12746.752| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.93 r_work: 0.3302 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12281 Z= 0.114 Angle : 0.496 7.055 16709 Z= 0.261 Chirality : 0.039 0.143 1953 Planarity : 0.004 0.048 2013 Dihedral : 5.175 55.206 2256 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.47 % Allowed : 6.40 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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 aren not related in a simple way. whole: 2.03 (0.21), residues: 1462 helix: 2.97 (0.18), residues: 690 sheet: 0.75 (0.30), residues: 281 loop : -0.74 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 87 TYR 0.017 0.001 TYR E 191 PHE 0.011 0.001 PHE B 199 TRP 0.021 0.002 TRP B 82 HIS 0.003 0.001 HIS R 321 Details of bonding type rmsd covalent geometry : bond 0.00245 (12278) covalent geometry : angle 0.49537 (16703) SS BOND : bond 0.00394 ( 3) SS BOND : angle 1.08652 ( 6) hydrogen bonds : bond 0.04083 ( 699) hydrogen bonds : angle 4.45585 ( 2034) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.7462 (mmm) cc_final: 0.7122 (mmm) REVERT: R 163 MET cc_start: 0.8741 (mtp) cc_final: 0.8479 (mtp) REVERT: R 335 PRO cc_start: 0.9038 (Cg_exo) cc_final: 0.8766 (Cg_endo) REVERT: B 98 SER cc_start: 0.8971 (m) cc_final: 0.8766 (t) REVERT: B 154 ASP cc_start: 0.8666 (m-30) cc_final: 0.8392 (m-30) REVERT: C 38 MET cc_start: 0.7364 (mmm) cc_final: 0.6721 (mmm) REVERT: E 106 SER cc_start: 0.8551 (t) cc_final: 0.8285 (p) REVERT: E 159 SER cc_start: 0.8302 (t) cc_final: 0.8014 (p) REVERT: E 187 GLN cc_start: 0.8346 (pt0) cc_final: 0.8109 (pt0) REVERT: M 341 LEU cc_start: 0.7540 (mm) cc_final: 0.7133 (tt) outliers start: 19 outliers final: 11 residues processed: 172 average time/residue: 0.1192 time to fit residues: 29.3652 Evaluate side-chains 145 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 180 GLN Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 0.0770 chunk 109 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.0070 chunk 93 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN B 340 ASN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.176540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.142100 restraints weight = 13061.618| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.06 r_work: 0.3249 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12281 Z= 0.099 Angle : 0.460 5.799 16709 Z= 0.243 Chirality : 0.038 0.141 1953 Planarity : 0.004 0.043 2013 Dihedral : 4.862 50.492 2256 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.70 % Allowed : 7.33 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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 aren not related in a simple way. whole: 2.21 (0.21), residues: 1462 helix: 3.24 (0.18), residues: 688 sheet: 0.62 (0.30), residues: 278 loop : -0.67 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 87 TYR 0.014 0.001 TYR M 151 PHE 0.008 0.001 PHE A 189 TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00208 (12278) covalent geometry : angle 0.46019 (16703) SS BOND : bond 0.00424 ( 3) SS BOND : angle 0.92303 ( 6) hydrogen bonds : bond 0.03745 ( 699) hydrogen bonds : angle 4.19824 ( 2034) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: R 74 MET cc_start: 0.7549 (mmm) cc_final: 0.7329 (mmm) REVERT: R 163 MET cc_start: 0.8762 (mtp) cc_final: 0.8499 (mtp) REVERT: R 335 PRO cc_start: 0.9018 (Cg_exo) cc_final: 0.8758 (Cg_endo) REVERT: A 230 TYR cc_start: 0.7559 (p90) cc_final: 0.7150 (p90) REVERT: A 315 ASP cc_start: 0.7568 (m-30) cc_final: 0.7263 (p0) REVERT: B 98 SER cc_start: 0.8989 (m) cc_final: 0.8743 (t) REVERT: B 154 ASP cc_start: 0.8680 (m-30) cc_final: 0.8397 (m-30) REVERT: B 198 LEU cc_start: 0.8295 (mp) cc_final: 0.8083 (mt) REVERT: E 87 ARG cc_start: 0.6604 (ttm110) cc_final: 0.6050 (mtm180) REVERT: E 93 MET cc_start: 0.7946 (tpp) cc_final: 0.7668 (tpp) REVERT: E 106 SER cc_start: 0.8711 (t) cc_final: 0.8379 (p) REVERT: E 155 SER cc_start: 0.7679 (p) cc_final: 0.7394 (t) REVERT: E 159 SER cc_start: 0.8245 (t) cc_final: 0.7953 (p) REVERT: M 341 LEU cc_start: 0.7662 (mm) cc_final: 0.7201 (tt) outliers start: 22 outliers final: 12 residues processed: 164 average time/residue: 0.1044 time to fit residues: 25.6909 Evaluate side-chains 153 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 332 CYS Chi-restraints excluded: chain M residue 337 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 52 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN E 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.166181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.129229 restraints weight = 12925.363| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.07 r_work: 0.3118 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12281 Z= 0.147 Angle : 0.521 7.175 16709 Z= 0.272 Chirality : 0.040 0.142 1953 Planarity : 0.004 0.041 2013 Dihedral : 5.305 47.143 2256 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.85 % Allowed : 8.18 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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 aren not related in a simple way. whole: 2.14 (0.21), residues: 1462 helix: 3.20 (0.18), residues: 686 sheet: 0.46 (0.30), residues: 279 loop : -0.63 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 265 TYR 0.016 0.002 TYR E 94 PHE 0.012 0.001 PHE E 240 TRP 0.021 0.002 TRP B 82 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00347 (12278) covalent geometry : angle 0.52022 (16703) SS BOND : bond 0.00280 ( 3) SS BOND : angle 1.05554 ( 6) hydrogen bonds : bond 0.04507 ( 699) hydrogen bonds : angle 4.35713 ( 2034) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: R 74 MET cc_start: 0.7607 (mmm) cc_final: 0.7337 (mmm) REVERT: R 147 SER cc_start: 0.8522 (t) cc_final: 0.8212 (m) REVERT: R 163 MET cc_start: 0.8852 (mtp) cc_final: 0.8581 (mtp) REVERT: A 193 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.7977 (t0) REVERT: A 230 TYR cc_start: 0.7810 (p90) cc_final: 0.7505 (p90) REVERT: A 315 ASP cc_start: 0.7830 (m-30) cc_final: 0.7413 (p0) REVERT: B 154 ASP cc_start: 0.8761 (m-30) cc_final: 0.8481 (m-30) REVERT: B 198 LEU cc_start: 0.8511 (mp) cc_final: 0.8304 (mt) REVERT: E 159 SER cc_start: 0.8279 (t) cc_final: 0.7961 (p) REVERT: E 187 GLN cc_start: 0.8206 (pt0) cc_final: 0.7784 (pt0) REVERT: M 341 LEU cc_start: 0.7683 (mm) cc_final: 0.7268 (tt) outliers start: 24 outliers final: 18 residues processed: 161 average time/residue: 0.1091 time to fit residues: 26.0337 Evaluate side-chains 155 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 142 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.167698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.130315 restraints weight = 13009.518| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.20 r_work: 0.3133 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12281 Z= 0.111 Angle : 0.472 8.036 16709 Z= 0.246 Chirality : 0.038 0.141 1953 Planarity : 0.003 0.038 2013 Dihedral : 5.056 50.913 2256 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.62 % Allowed : 9.34 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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 aren not related in a simple way. whole: 2.21 (0.22), residues: 1462 helix: 3.27 (0.18), residues: 683 sheet: 0.43 (0.29), residues: 289 loop : -0.56 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 219 TYR 0.011 0.001 TYR E 191 PHE 0.011 0.001 PHE B 292 TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00249 (12278) covalent geometry : angle 0.47164 (16703) SS BOND : bond 0.00390 ( 3) SS BOND : angle 0.76267 ( 6) hydrogen bonds : bond 0.03919 ( 699) hydrogen bonds : angle 4.19184 ( 2034) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: R 74 MET cc_start: 0.7458 (mmm) cc_final: 0.7227 (mmm) REVERT: R 163 MET cc_start: 0.8703 (mtp) cc_final: 0.8402 (mtp) REVERT: R 205 MET cc_start: 0.8866 (ttm) cc_final: 0.8558 (ttp) REVERT: R 218 ASP cc_start: 0.7980 (m-30) cc_final: 0.7024 (p0) REVERT: R 341 LEU cc_start: 0.8510 (mm) cc_final: 0.8087 (mt) REVERT: A 230 TYR cc_start: 0.7820 (p90) cc_final: 0.7556 (p90) REVERT: B 154 ASP cc_start: 0.8512 (m-30) cc_final: 0.8232 (m-30) REVERT: E 93 MET cc_start: 0.7564 (tpp) cc_final: 0.7362 (tpp) REVERT: E 159 SER cc_start: 0.8130 (t) cc_final: 0.7868 (p) REVERT: M 74 MET cc_start: 0.7271 (mmm) cc_final: 0.7047 (tpp) REVERT: M 341 LEU cc_start: 0.7744 (mm) cc_final: 0.7239 (tt) outliers start: 21 outliers final: 17 residues processed: 152 average time/residue: 0.1160 time to fit residues: 25.8189 Evaluate side-chains 151 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 0 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.166853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.129626 restraints weight = 12964.728| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.24 r_work: 0.3122 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12281 Z= 0.114 Angle : 0.479 9.301 16709 Z= 0.247 Chirality : 0.038 0.197 1953 Planarity : 0.003 0.038 2013 Dihedral : 5.071 52.782 2256 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.77 % Allowed : 9.88 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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 aren not related in a simple way. whole: 2.24 (0.22), residues: 1462 helix: 3.28 (0.18), residues: 685 sheet: 0.40 (0.30), residues: 289 loop : -0.51 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 87 TYR 0.011 0.001 TYR E 191 PHE 0.011 0.001 PHE B 199 TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS R 321 Details of bonding type rmsd covalent geometry : bond 0.00260 (12278) covalent geometry : angle 0.47920 (16703) SS BOND : bond 0.00331 ( 3) SS BOND : angle 0.71211 ( 6) hydrogen bonds : bond 0.03908 ( 699) hydrogen bonds : angle 4.14634 ( 2034) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: R 74 MET cc_start: 0.7503 (mmm) cc_final: 0.7270 (mmm) REVERT: R 147 SER cc_start: 0.8288 (t) cc_final: 0.7983 (m) REVERT: R 163 MET cc_start: 0.8693 (mtp) cc_final: 0.8395 (mtp) REVERT: R 205 MET cc_start: 0.8880 (ttm) cc_final: 0.8547 (ttp) REVERT: R 218 ASP cc_start: 0.8000 (m-30) cc_final: 0.7115 (p0) REVERT: R 341 LEU cc_start: 0.8648 (mm) cc_final: 0.8177 (mt) REVERT: A 230 TYR cc_start: 0.7967 (p90) cc_final: 0.7720 (p90) REVERT: B 70 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8840 (pt) REVERT: B 154 ASP cc_start: 0.8484 (m-30) cc_final: 0.8221 (m-30) REVERT: C 38 MET cc_start: 0.7234 (mmm) cc_final: 0.6925 (mmm) REVERT: E 93 MET cc_start: 0.7630 (tpp) cc_final: 0.7397 (tpp) REVERT: E 159 SER cc_start: 0.8154 (t) cc_final: 0.7914 (p) REVERT: M 341 LEU cc_start: 0.7677 (mm) cc_final: 0.7291 (tt) outliers start: 23 outliers final: 19 residues processed: 159 average time/residue: 0.1157 time to fit residues: 27.0232 Evaluate side-chains 160 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.4977 > 50: distance: 12 - 158: 30.197 distance: 15 - 155: 16.603 distance: 85 - 91: 16.539 distance: 91 - 92: 19.897 distance: 91 - 166: 28.494 distance: 92 - 93: 24.873 distance: 92 - 95: 18.727 distance: 93 - 94: 12.306 distance: 93 - 97: 6.188 distance: 94 - 163: 30.123 distance: 95 - 96: 39.917 distance: 97 - 98: 4.596 distance: 98 - 99: 13.018 distance: 98 - 101: 21.096 distance: 99 - 100: 21.468 distance: 99 - 108: 28.479 distance: 101 - 102: 16.877 distance: 102 - 103: 11.617 distance: 103 - 104: 22.949 distance: 104 - 105: 9.849 distance: 105 - 106: 7.006 distance: 105 - 107: 21.539 distance: 108 - 109: 15.746 distance: 108 - 151: 52.527 distance: 109 - 110: 19.585 distance: 109 - 112: 16.339 distance: 110 - 111: 33.074 distance: 110 - 116: 22.957 distance: 111 - 148: 34.084 distance: 112 - 113: 17.109 distance: 113 - 114: 36.652 distance: 113 - 115: 24.383 distance: 116 - 117: 4.376 distance: 117 - 118: 13.805 distance: 117 - 120: 44.039 distance: 118 - 119: 14.926 distance: 118 - 124: 40.741 distance: 120 - 121: 11.609 distance: 121 - 122: 16.134 distance: 121 - 123: 47.180 distance: 124 - 125: 17.583 distance: 124 - 130: 29.044 distance: 125 - 126: 11.546 distance: 125 - 128: 11.584 distance: 126 - 127: 14.236 distance: 126 - 131: 14.296 distance: 128 - 129: 10.804 distance: 129 - 130: 6.439 distance: 131 - 132: 4.893 distance: 132 - 133: 19.528 distance: 132 - 135: 17.996 distance: 133 - 134: 14.115 distance: 133 - 140: 22.531 distance: 135 - 136: 22.222 distance: 136 - 137: 19.963 distance: 137 - 138: 12.613 distance: 138 - 139: 21.201 distance: 140 - 141: 17.881 distance: 141 - 142: 28.635 distance: 141 - 144: 30.364 distance: 142 - 143: 6.106 distance: 142 - 148: 15.221 distance: 144 - 145: 24.364 distance: 145 - 146: 23.099 distance: 145 - 147: 18.834 distance: 148 - 149: 19.404 distance: 149 - 150: 8.689 distance: 149 - 152: 24.538 distance: 150 - 151: 18.485 distance: 150 - 155: 13.937 distance: 152 - 153: 25.732 distance: 152 - 154: 19.670 distance: 155 - 156: 17.927 distance: 156 - 157: 19.912 distance: 156 - 159: 4.716 distance: 157 - 158: 10.062 distance: 157 - 163: 6.463 distance: 159 - 160: 16.635 distance: 160 - 161: 16.234 distance: 160 - 162: 24.436 distance: 163 - 164: 3.316 distance: 164 - 165: 21.887 distance: 164 - 167: 25.027 distance: 165 - 166: 10.271 distance: 165 - 174: 26.481 distance: 167 - 168: 8.932 distance: 168 - 169: 30.220 distance: 168 - 170: 11.953 distance: 169 - 171: 20.538 distance: 170 - 172: 14.398 distance: 171 - 173: 23.279 distance: 172 - 173: 17.470