Starting phenix.real_space_refine on Mon Apr 28 01:15:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m71_23707/04_2025/7m71_23707.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m71_23707/04_2025/7m71_23707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m71_23707/04_2025/7m71_23707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m71_23707/04_2025/7m71_23707.map" model { file = "/net/cci-nas-00/data/ceres_data/7m71_23707/04_2025/7m71_23707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m71_23707/04_2025/7m71_23707.cif" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.072 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 29 5.16 5 C 4212 2.51 5 N 1112 2.21 5 O 1293 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6646 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1657 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain: "B" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1657 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain: "H" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1645 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain: "L" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1631 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 202} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.68, per 1000 atoms: 0.70 Number of scatterers: 6646 At special positions: 0 Unit cell: (115.193, 92.6293, 129.444, 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 29 16.00 O 1293 8.00 N 1112 7.00 C 4212 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.07 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.07 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS H 222 " - pdb=" SG CYS L 214 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.07 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 946.7 milliseconds 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1574 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 20 sheets defined 14.0% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.941A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.606A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.446A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.860A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.715A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.504A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.222A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 162 through 164 No H-bonds generated for 'chain 'H' and resid 162 through 164' Processing helix chain 'H' and resid 191 through 197 removed outlier: 4.268A pdb=" N GLY H 196 " --> pdb=" O SER H 193 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.906A pdb=" N LYS L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 153 Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.703A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.699A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.761A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.776A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.893A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLY H 145 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL H 188 " --> pdb=" O GLY H 145 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU H 147 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N SER H 186 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LYS H 149 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU H 184 " --> pdb=" O LYS H 149 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR H 151 " --> pdb=" O TYR H 182 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 137 through 138 removed outlier: 5.283A pdb=" N GLY H 145 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL H 188 " --> pdb=" O GLY H 145 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU H 147 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N SER H 186 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LYS H 149 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU H 184 " --> pdb=" O LYS H 149 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR H 151 " --> pdb=" O TYR H 182 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 156 through 160 Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.410A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 117 through 118 Processing sheet with id=AB9, first strand: chain 'L' and resid 129 through 131 Processing sheet with id=AC1, first strand: chain 'L' and resid 145 through 148 Processing sheet with id=AC2, first strand: chain 'L' and resid 161 through 164 removed outlier: 4.153A pdb=" N SER L 174 " --> pdb=" O THR L 164 " (cutoff:3.500A) 207 hydrogen bonds defined for protein. 465 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: 1.91 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1616 1.33 - 1.45: 1469 1.45 - 1.58: 3693 1.58 - 1.70: 0 1.70 - 1.82: 32 Bond restraints: 6810 Sorted by residual: bond pdb=" CA PHE L 118 " pdb=" C PHE L 118 " ideal model delta sigma weight residual 1.522 1.564 -0.042 1.06e-02 8.90e+03 1.55e+01 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.413 1.486 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" CZ ARG A 454 " pdb=" NH2 ARG A 454 " ideal model delta sigma weight residual 1.330 1.285 0.045 1.30e-02 5.92e+03 1.22e+01 bond pdb=" C5 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.413 1.482 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" CA PRO L 119 " pdb=" C PRO L 119 " ideal model delta sigma weight residual 1.517 1.549 -0.032 9.30e-03 1.16e+04 1.18e+01 ... (remaining 6805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 6411 1.84 - 3.69: 2379 3.69 - 5.53: 420 5.53 - 7.38: 41 7.38 - 9.22: 7 Bond angle restraints: 9258 Sorted by residual: angle pdb=" CA PHE H 68 " pdb=" CB PHE H 68 " pdb=" CG PHE H 68 " ideal model delta sigma weight residual 113.80 121.12 -7.32 1.00e+00 1.00e+00 5.36e+01 angle pdb=" CA GLY A 416 " pdb=" C GLY A 416 " pdb=" N LYS A 417 " ideal model delta sigma weight residual 114.23 120.16 -5.93 8.80e-01 1.29e+00 4.54e+01 angle pdb=" CB ASN A 331 " pdb=" CG ASN A 331 " pdb=" ND2 ASN A 331 " ideal model delta sigma weight residual 116.40 107.47 8.93 1.50e+00 4.44e-01 3.54e+01 angle pdb=" C LYS H 215 " pdb=" N LYS H 216 " pdb=" CA LYS H 216 " ideal model delta sigma weight residual 120.95 128.90 -7.95 1.40e+00 5.10e-01 3.22e+01 angle pdb=" CA PHE L 209 " pdb=" CB PHE L 209 " pdb=" CG PHE L 209 " ideal model delta sigma weight residual 113.80 119.13 -5.33 1.00e+00 1.00e+00 2.84e+01 ... (remaining 9253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 3785 17.69 - 35.37: 271 35.37 - 53.05: 45 53.05 - 70.74: 10 70.74 - 88.42: 4 Dihedral angle restraints: 4115 sinusoidal: 1642 harmonic: 2473 Sorted by residual: dihedral pdb=" CA THR L 178 " pdb=" C THR L 178 " pdb=" N LEU L 179 " pdb=" CA LEU L 179 " ideal model delta harmonic sigma weight residual 180.00 150.15 29.85 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA ARG H 72 " pdb=" C ARG H 72 " pdb=" N ASP H 73 " pdb=" CA ASP H 73 " ideal model delta harmonic sigma weight residual 180.00 150.43 29.57 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA LEU L 104 " pdb=" C LEU L 104 " pdb=" N GLU L 105 " pdb=" CA GLU L 105 " ideal model delta harmonic sigma weight residual -180.00 -150.73 -29.27 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 4112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.274: 1010 0.274 - 0.548: 13 0.548 - 0.822: 0 0.822 - 1.096: 0 1.096 - 1.370: 1 Chirality restraints: 1024 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.03 -1.37 2.00e-01 2.50e+01 4.69e+01 chirality pdb=" CA ASP H 150 " pdb=" N ASP H 150 " pdb=" C ASP H 150 " pdb=" CB ASP H 150 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CA ASN B 331 " pdb=" N ASN B 331 " pdb=" C ASN B 331 " pdb=" CB ASN B 331 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.06e+00 ... (remaining 1021 not shown) Planarity restraints: 1197 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.098 2.00e-02 2.50e+03 1.02e-01 1.31e+02 pdb=" CG ASN A 331 " 0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.153 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 49 " 0.131 2.00e-02 2.50e+03 7.39e-02 1.09e+02 pdb=" CG TYR L 49 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR L 49 " -0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR L 49 " -0.065 2.00e-02 2.50e+03 pdb=" CE1 TYR L 49 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR L 49 " -0.039 2.00e-02 2.50e+03 pdb=" CZ TYR L 49 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR L 49 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 353 " -0.121 2.00e-02 2.50e+03 6.35e-02 1.01e+02 pdb=" CG TRP B 353 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP B 353 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP B 353 " 0.091 2.00e-02 2.50e+03 pdb=" NE1 TRP B 353 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP B 353 " 0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP B 353 " 0.085 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 353 " -0.051 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 353 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B 353 " -0.074 2.00e-02 2.50e+03 ... (remaining 1194 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 3298 3.00 - 3.48: 6121 3.48 - 3.95: 11157 3.95 - 4.43: 12531 4.43 - 4.90: 20762 Nonbonded interactions: 53869 Sorted by model distance: nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.531 3.040 nonbonded pdb=" OE1 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.549 3.040 nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.561 3.040 nonbonded pdb=" OD1 ASP B 467 " pdb=" OG SER B 469 " model vdw 2.577 3.040 nonbonded pdb=" OG SER B 438 " pdb=" OD2 ASP B 442 " model vdw 2.579 3.040 ... (remaining 53864 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 3.040 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.820 Find NCS groups from input model: 0.160 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:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 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 : 0.013 0.073 6827 Z= 0.752 Angle : 1.872 9.869 9296 Z= 1.236 Chirality : 0.112 1.370 1024 Planarity : 0.016 0.190 1193 Dihedral : 12.979 88.419 2502 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 0.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.41 % Allowed : 3.81 % Favored : 95.78 % Cbeta Deviations : 0.64 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.27), residues: 844 helix: -4.22 (0.28), residues: 79 sheet: 0.09 (0.32), residues: 253 loop : -0.31 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.121 0.024 TRP B 353 HIS 0.007 0.003 HIS H 206 PHE 0.077 0.013 PHE L 118 TYR 0.131 0.019 TYR L 49 ARG 0.011 0.001 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00964 ( 4) link_NAG-ASN : angle 5.38630 ( 12) hydrogen bonds : bond 0.12603 ( 199) hydrogen bonds : angle 9.08133 ( 465) SS BOND : bond 0.02022 ( 13) SS BOND : angle 2.54002 ( 26) covalent geometry : bond 0.01282 ( 6810) covalent geometry : angle 1.86108 ( 9258) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.702 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 56 average time/residue: 1.6921 time to fit residues: 99.0017 Evaluate side-chains 27 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 165 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN A 487 ASN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.053945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.034501 restraints weight = 33051.369| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.46 r_work: 0.2738 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6827 Z= 0.133 Angle : 0.649 7.707 9296 Z= 0.340 Chirality : 0.045 0.155 1024 Planarity : 0.005 0.039 1193 Dihedral : 6.279 47.915 1017 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.82 % Allowed : 7.21 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.29), residues: 844 helix: -3.30 (0.54), residues: 65 sheet: 0.10 (0.30), residues: 285 loop : -0.02 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 436 HIS 0.001 0.000 HIS A 519 PHE 0.015 0.001 PHE H 29 TYR 0.024 0.001 TYR L 186 ARG 0.007 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 4) link_NAG-ASN : angle 3.16917 ( 12) hydrogen bonds : bond 0.03733 ( 199) hydrogen bonds : angle 7.07477 ( 465) SS BOND : bond 0.00325 ( 13) SS BOND : angle 0.76650 ( 26) covalent geometry : bond 0.00291 ( 6810) covalent geometry : angle 0.63893 ( 9258) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.775 Fit side-chains REVERT: A 406 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8552 (mt-10) REVERT: B 340 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8658 (mp0) outliers start: 6 outliers final: 2 residues processed: 38 average time/residue: 1.7211 time to fit residues: 68.9566 Evaluate side-chains 27 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain L residue 134 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 68 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 39 optimal weight: 0.0000 chunk 44 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 22 optimal weight: 0.0570 chunk 3 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 198 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.053483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.034183 restraints weight = 33473.624| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 3.45 r_work: 0.2742 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6827 Z= 0.114 Angle : 0.559 6.718 9296 Z= 0.289 Chirality : 0.044 0.143 1024 Planarity : 0.004 0.041 1193 Dihedral : 5.300 50.353 1014 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.27 % Allowed : 8.84 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.29), residues: 844 helix: -2.91 (0.59), residues: 65 sheet: 0.36 (0.30), residues: 277 loop : 0.09 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.002 0.001 HIS L 198 PHE 0.011 0.001 PHE H 29 TYR 0.016 0.001 TYR A 495 ARG 0.008 0.001 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 4) link_NAG-ASN : angle 2.25787 ( 12) hydrogen bonds : bond 0.03228 ( 199) hydrogen bonds : angle 6.36778 ( 465) SS BOND : bond 0.00284 ( 13) SS BOND : angle 0.72587 ( 26) covalent geometry : bond 0.00255 ( 6810) covalent geometry : angle 0.55309 ( 9258) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.756 Fit side-chains REVERT: A 406 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8503 (mt-10) REVERT: B 340 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8685 (mp0) REVERT: B 516 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8132 (pp20) REVERT: L 105 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7881 (mp0) REVERT: L 142 ARG cc_start: 0.9064 (ttp80) cc_final: 0.8600 (ttp80) outliers start: 2 outliers final: 1 residues processed: 32 average time/residue: 1.5795 time to fit residues: 53.4464 Evaluate side-chains 29 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain L residue 154 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 59 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 0.0870 chunk 56 optimal weight: 6.9990 chunk 74 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 overall best weight: 3.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.051622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.032285 restraints weight = 34146.176| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 3.54 r_work: 0.2669 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 6827 Z= 0.312 Angle : 0.646 6.967 9296 Z= 0.335 Chirality : 0.046 0.144 1024 Planarity : 0.005 0.042 1193 Dihedral : 5.954 47.975 1014 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.09 % Allowed : 9.52 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.29), residues: 844 helix: -3.11 (0.51), residues: 72 sheet: 0.12 (0.30), residues: 286 loop : -0.10 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 HIS 0.003 0.001 HIS A 519 PHE 0.015 0.002 PHE L 83 TYR 0.019 0.002 TYR L 186 ARG 0.007 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 4) link_NAG-ASN : angle 2.93770 ( 12) hydrogen bonds : bond 0.03851 ( 199) hydrogen bonds : angle 6.67514 ( 465) SS BOND : bond 0.00495 ( 13) SS BOND : angle 1.00698 ( 26) covalent geometry : bond 0.00718 ( 6810) covalent geometry : angle 0.63589 ( 9258) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8697 (mp0) REVERT: B 516 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8141 (pp20) REVERT: L 142 ARG cc_start: 0.9149 (ttp80) cc_final: 0.8742 (ttp80) outliers start: 8 outliers final: 4 residues processed: 33 average time/residue: 1.4668 time to fit residues: 51.4063 Evaluate side-chains 29 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain L residue 134 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.6619 > 50: distance: 72 - 95: 34.275 distance: 75 - 82: 27.511 distance: 76 - 103: 34.970 distance: 82 - 83: 24.173 distance: 83 - 84: 15.191 distance: 83 - 86: 19.903 distance: 84 - 85: 39.730 distance: 85 - 115: 34.170 distance: 86 - 87: 43.455 distance: 86 - 88: 20.784 distance: 91 - 92: 3.708 distance: 91 - 94: 22.562 distance: 92 - 93: 5.268 distance: 92 - 95: 4.077 distance: 95 - 96: 19.589 distance: 96 - 97: 19.375 distance: 96 - 99: 21.607 distance: 100 - 102: 39.564 distance: 105 - 115: 6.079 distance: 107 - 108: 3.922 distance: 108 - 109: 30.805 distance: 108 - 110: 9.948 distance: 109 - 111: 39.271 distance: 111 - 113: 38.983 distance: 112 - 113: 19.176 distance: 113 - 114: 30.885 distance: 115 - 116: 33.779 distance: 116 - 117: 36.393 distance: 116 - 119: 34.682 distance: 117 - 123: 49.181 distance: 119 - 120: 33.904 distance: 120 - 121: 23.176 distance: 120 - 122: 20.644 distance: 123 - 124: 48.682 distance: 124 - 127: 36.724 distance: 125 - 126: 40.636 distance: 127 - 128: 39.991 distance: 128 - 130: 49.451 distance: 129 - 131: 15.020 distance: 130 - 132: 27.366 distance: 132 - 133: 42.648 distance: 133 - 134: 40.177 distance: 135 - 136: 39.279 distance: 136 - 137: 34.439 distance: 137 - 138: 7.070 distance: 137 - 144: 41.081 distance: 140 - 141: 38.020 distance: 144 - 145: 53.119 distance: 145 - 146: 36.846 distance: 145 - 148: 34.162 distance: 146 - 147: 32.119 distance: 146 - 152: 52.228 distance: 148 - 149: 41.238 distance: 149 - 151: 8.250 distance: 152 - 153: 39.880 distance: 152 - 158: 9.046 distance: 153 - 154: 40.787 distance: 154 - 159: 39.780 distance: 156 - 157: 40.534 distance: 157 - 158: 11.238 distance: 159 - 160: 31.932 distance: 160 - 161: 57.957 distance: 160 - 163: 42.464 distance: 161 - 162: 19.801 distance: 161 - 167: 28.407 distance: 163 - 164: 38.783 distance: 164 - 166: 39.525