Starting phenix.real_space_refine on Tue Jun 25 17:48:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blo_16110/06_2024/8blo_16110_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blo_16110/06_2024/8blo_16110.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blo_16110/06_2024/8blo_16110_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blo_16110/06_2024/8blo_16110_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blo_16110/06_2024/8blo_16110_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blo_16110/06_2024/8blo_16110.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blo_16110/06_2024/8blo_16110.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blo_16110/06_2024/8blo_16110_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blo_16110/06_2024/8blo_16110_updated.pdb" } resolution = 2.9 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= 0.152 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 51 5.16 5 C 5724 2.51 5 N 1239 2.21 5 O 1470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 104": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C GLU 339": "OE1" <-> "OE2" Residue "C PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 383": "OE1" <-> "OE2" Residue "C TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B GLU 339": "OE1" <-> "OE2" Residue "B PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 8487 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2646 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 19, 'TRANS': 332} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2646 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 19, 'TRANS': 332} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2646 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 19, 'TRANS': 332} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 177 Unusual residues: {'LMN': 5, 'PLD': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 367 Unresolved non-hydrogen angles: 506 Unresolved non-hydrogen dihedrals: 606 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'PLD:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 177 Unusual residues: {'LMN': 5, 'PLD': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 367 Unresolved non-hydrogen angles: 506 Unresolved non-hydrogen dihedrals: 606 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'PLD:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 177 Unusual residues: {'LMN': 5, 'PLD': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 367 Unresolved non-hydrogen angles: 506 Unresolved non-hydrogen dihedrals: 606 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'PLD:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 5.54, per 1000 atoms: 0.65 Number of scatterers: 8487 At special positions: 0 Unit cell: (97.58, 103.32, 72.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 P 3 15.00 O 1470 8.00 N 1239 7.00 C 5724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.22 Conformation dependent library (CDL) restraints added in 1.5 seconds 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 0 sheets defined 67.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 94 through 97 No H-bonds generated for 'chain 'A' and resid 94 through 97' Processing helix chain 'A' and resid 103 through 111 removed outlier: 4.579A pdb=" N ASP A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 130 removed outlier: 3.968A pdb=" N VAL A 129 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N MET A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 150 through 169 Processing helix chain 'A' and resid 174 through 177 No H-bonds generated for 'chain 'A' and resid 174 through 177' Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 204 through 230 Proline residue: A 209 - end of helix removed outlier: 4.032A pdb=" N MET A 215 " --> pdb=" O PHE A 212 " (cutoff:3.500A) Proline residue: A 218 - end of helix removed outlier: 3.551A pdb=" N LEU A 224 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER A 229 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 230 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 250 Processing helix chain 'A' and resid 279 through 293 removed outlier: 4.003A pdb=" N ILE A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Proline residue: A 287 - end of helix removed outlier: 4.053A pdb=" N VAL A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 312 Processing helix chain 'A' and resid 314 through 334 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 348 through 357 removed outlier: 3.811A pdb=" N LEU A 352 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER A 353 " --> pdb=" O ASN A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 390 Processing helix chain 'A' and resid 400 through 411 Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'C' and resid 94 through 97 No H-bonds generated for 'chain 'C' and resid 94 through 97' Processing helix chain 'C' and resid 103 through 111 removed outlier: 4.580A pdb=" N ASP C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 130 removed outlier: 3.967A pdb=" N VAL C 129 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N MET C 130 " --> pdb=" O THR C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 148 Processing helix chain 'C' and resid 150 through 169 Processing helix chain 'C' and resid 174 through 177 No H-bonds generated for 'chain 'C' and resid 174 through 177' Processing helix chain 'C' and resid 184 through 195 Processing helix chain 'C' and resid 204 through 230 Proline residue: C 209 - end of helix removed outlier: 4.032A pdb=" N MET C 215 " --> pdb=" O PHE C 212 " (cutoff:3.500A) Proline residue: C 218 - end of helix removed outlier: 3.550A pdb=" N LEU C 224 " --> pdb=" O SER C 221 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER C 229 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS C 230 " --> pdb=" O ILE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 250 Processing helix chain 'C' and resid 279 through 293 removed outlier: 4.003A pdb=" N ILE C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) Proline residue: C 287 - end of helix removed outlier: 4.054A pdb=" N VAL C 293 " --> pdb=" O GLY C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 312 Processing helix chain 'C' and resid 314 through 334 Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 348 through 357 removed outlier: 3.809A pdb=" N LEU C 352 " --> pdb=" O TYR C 348 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER C 353 " --> pdb=" O ASN C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 390 Processing helix chain 'C' and resid 400 through 411 Processing helix chain 'C' and resid 424 through 426 No H-bonds generated for 'chain 'C' and resid 424 through 426' Processing helix chain 'C' and resid 430 through 441 Processing helix chain 'B' and resid 94 through 97 No H-bonds generated for 'chain 'B' and resid 94 through 97' Processing helix chain 'B' and resid 103 through 111 removed outlier: 4.579A pdb=" N ASP B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 130 removed outlier: 3.968A pdb=" N VAL B 129 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N MET B 130 " --> pdb=" O THR B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 148 Processing helix chain 'B' and resid 150 through 169 Processing helix chain 'B' and resid 174 through 177 No H-bonds generated for 'chain 'B' and resid 174 through 177' Processing helix chain 'B' and resid 184 through 195 Processing helix chain 'B' and resid 204 through 230 Proline residue: B 209 - end of helix removed outlier: 4.032A pdb=" N MET B 215 " --> pdb=" O PHE B 212 " (cutoff:3.500A) Proline residue: B 218 - end of helix removed outlier: 3.550A pdb=" N LEU B 224 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER B 229 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS B 230 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 250 Processing helix chain 'B' and resid 279 through 293 removed outlier: 4.003A pdb=" N ILE B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Proline residue: B 287 - end of helix removed outlier: 4.052A pdb=" N VAL B 293 " --> pdb=" O GLY B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 312 Processing helix chain 'B' and resid 314 through 334 Processing helix chain 'B' and resid 338 through 342 Processing helix chain 'B' and resid 348 through 357 removed outlier: 3.809A pdb=" N LEU B 352 " --> pdb=" O TYR B 348 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER B 353 " --> pdb=" O ASN B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 390 Processing helix chain 'B' and resid 400 through 411 Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing helix chain 'B' and resid 430 through 441 441 hydrogen bonds defined for protein. 1197 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: 2.38 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1209 1.31 - 1.43: 2317 1.43 - 1.56: 4957 1.56 - 1.68: 124 1.68 - 1.81: 78 Bond restraints: 8685 Sorted by residual: bond pdb=" CD' PLD A1003 " pdb=" CE' PLD A1003 " ideal model delta sigma weight residual 1.526 1.578 -0.052 2.00e-02 2.50e+03 6.84e+00 bond pdb=" CD' PLD B1003 " pdb=" CE' PLD B1003 " ideal model delta sigma weight residual 1.526 1.578 -0.052 2.00e-02 2.50e+03 6.75e+00 bond pdb=" CD' PLD A1002 " pdb=" CE' PLD A1002 " ideal model delta sigma weight residual 1.526 1.578 -0.052 2.00e-02 2.50e+03 6.74e+00 bond pdb=" CF' PLD B1003 " pdb=" CG' PLD B1003 " ideal model delta sigma weight residual 1.527 1.578 -0.051 2.00e-02 2.50e+03 6.62e+00 bond pdb=" CF' PLD A1003 " pdb=" CG' PLD A1003 " ideal model delta sigma weight residual 1.527 1.578 -0.051 2.00e-02 2.50e+03 6.61e+00 ... (remaining 8680 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.38: 299 106.38 - 113.29: 4862 113.29 - 120.20: 3134 120.20 - 127.11: 3354 127.11 - 134.02: 141 Bond angle restraints: 11790 Sorted by residual: angle pdb=" C VAL A 235 " pdb=" N PHE A 236 " pdb=" CA PHE A 236 " ideal model delta sigma weight residual 121.54 128.36 -6.82 1.91e+00 2.74e-01 1.27e+01 angle pdb=" C VAL B 235 " pdb=" N PHE B 236 " pdb=" CA PHE B 236 " ideal model delta sigma weight residual 121.54 128.31 -6.77 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C VAL C 235 " pdb=" N PHE C 236 " pdb=" CA PHE C 236 " ideal model delta sigma weight residual 121.54 128.31 -6.77 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C VAL A 269 " pdb=" N PRO A 270 " pdb=" CA PRO A 270 " ideal model delta sigma weight residual 119.76 122.84 -3.08 1.03e+00 9.43e-01 8.91e+00 angle pdb=" C VAL C 269 " pdb=" N PRO C 270 " pdb=" CA PRO C 270 " ideal model delta sigma weight residual 119.76 122.83 -3.07 1.03e+00 9.43e-01 8.86e+00 ... (remaining 11785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.65: 4817 26.65 - 53.30: 201 53.30 - 79.94: 73 79.94 - 106.59: 6 106.59 - 133.24: 9 Dihedral angle restraints: 5106 sinusoidal: 2055 harmonic: 3051 Sorted by residual: dihedral pdb=" CBH LMN B1004 " pdb=" CBJ LMN B1004 " pdb=" CBL LMN B1004 " pdb=" CBR LMN B1004 " ideal model delta sinusoidal sigma weight residual 181.02 47.78 133.24 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" CBH LMN A1004 " pdb=" CBJ LMN A1004 " pdb=" CBL LMN A1004 " pdb=" CBR LMN A1004 " ideal model delta sinusoidal sigma weight residual 181.02 47.79 133.23 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" CBH LMN C1004 " pdb=" CBJ LMN C1004 " pdb=" CBL LMN C1004 " pdb=" CBR LMN C1004 " ideal model delta sinusoidal sigma weight residual 181.02 47.80 133.22 1 3.00e+01 1.11e-03 1.80e+01 ... (remaining 5103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 708 0.028 - 0.055: 413 0.055 - 0.083: 164 0.083 - 0.110: 60 0.110 - 0.138: 11 Chirality restraints: 1356 Sorted by residual: chirality pdb=" CA PRO B 430 " pdb=" N PRO B 430 " pdb=" C PRO B 430 " pdb=" CB PRO B 430 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA PRO C 430 " pdb=" N PRO C 430 " pdb=" C PRO C 430 " pdb=" CB PRO C 430 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA PRO A 430 " pdb=" N PRO A 430 " pdb=" C PRO A 430 " pdb=" CB PRO A 430 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 1353 not shown) Planarity restraints: 1383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 279 " 0.032 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO B 280 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 280 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 280 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 279 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO C 280 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 280 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 280 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 279 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO A 280 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 280 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 280 " 0.027 5.00e-02 4.00e+02 ... (remaining 1380 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2724 2.84 - 3.36: 8437 3.36 - 3.87: 15088 3.87 - 4.39: 18948 4.39 - 4.90: 30421 Nonbonded interactions: 75618 Sorted by model distance: nonbonded pdb=" O GLU A 339 " pdb=" OG1 THR A 343 " model vdw 2.328 2.440 nonbonded pdb=" O GLU C 339 " pdb=" OG1 THR C 343 " model vdw 2.328 2.440 nonbonded pdb=" O GLU B 339 " pdb=" OG1 THR B 343 " model vdw 2.328 2.440 nonbonded pdb=" OG1 THR C 164 " pdb=" O HOH C1101 " model vdw 2.435 2.440 nonbonded pdb=" OG SER C 353 " pdb=" SG CYS C 379 " model vdw 2.441 2.800 ... (remaining 75613 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 2.160 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: 5.850 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.750 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 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 : 0.007 0.052 8685 Z= 0.439 Angle : 0.686 6.817 11790 Z= 0.363 Chirality : 0.040 0.138 1356 Planarity : 0.005 0.048 1383 Dihedral : 17.375 133.242 3150 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.86 % Favored : 96.86 % Rotamer: Outliers : 0.98 % Allowed : 3.44 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.24), residues: 1050 helix: -0.73 (0.17), residues: 753 sheet: None (None), residues: 0 loop : -1.21 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 300 HIS 0.003 0.001 HIS B 319 PHE 0.016 0.002 PHE C 361 TYR 0.013 0.001 TYR A 184 ARG 0.001 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 0.885 Fit side-chains REVERT: B 387 SER cc_start: 0.8367 (t) cc_final: 0.8135 (m) outliers start: 8 outliers final: 1 residues processed: 101 average time/residue: 0.7877 time to fit residues: 87.7302 Evaluate side-chains 79 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 343 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 8.9990 chunk 79 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN C 415 ASN ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8685 Z= 0.182 Angle : 0.535 8.210 11790 Z= 0.259 Chirality : 0.040 0.152 1356 Planarity : 0.005 0.051 1383 Dihedral : 17.729 134.208 1567 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.60 % Allowed : 9.23 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.26), residues: 1050 helix: 0.35 (0.18), residues: 750 sheet: None (None), residues: 0 loop : -0.22 (0.40), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 108 HIS 0.002 0.001 HIS B 319 PHE 0.014 0.001 PHE B 361 TYR 0.011 0.001 TYR A 184 ARG 0.002 0.000 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.848 Fit side-chains REVERT: A 387 SER cc_start: 0.8470 (t) cc_final: 0.8156 (m) REVERT: C 119 ILE cc_start: 0.8303 (mt) cc_final: 0.7901 (mp) REVERT: B 408 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8110 (mt) outliers start: 13 outliers final: 3 residues processed: 98 average time/residue: 0.7814 time to fit residues: 84.6076 Evaluate side-chains 89 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain B residue 408 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 chunk 95 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN A 416 ASN C 415 ASN C 416 ASN B 415 ASN B 416 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8685 Z= 0.166 Angle : 0.519 7.698 11790 Z= 0.250 Chirality : 0.039 0.128 1356 Planarity : 0.005 0.051 1383 Dihedral : 16.305 135.943 1566 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.21 % Allowed : 10.82 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.27), residues: 1050 helix: 0.76 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.02 (0.41), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 108 HIS 0.002 0.001 HIS B 319 PHE 0.021 0.001 PHE B 378 TYR 0.010 0.001 TYR A 184 ARG 0.001 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 0.889 Fit side-chains REVERT: A 187 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8127 (tpp) REVERT: A 387 SER cc_start: 0.8337 (OUTLIER) cc_final: 0.8062 (m) REVERT: C 408 ILE cc_start: 0.8563 (mt) cc_final: 0.8204 (mt) REVERT: B 119 ILE cc_start: 0.8364 (mt) cc_final: 0.7960 (mp) REVERT: B 230 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8245 (mmmt) REVERT: B 408 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8109 (mt) outliers start: 18 outliers final: 7 residues processed: 104 average time/residue: 0.7506 time to fit residues: 86.4485 Evaluate side-chains 99 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 408 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 49 optimal weight: 0.0040 chunk 10 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN A 416 ASN C 415 ASN C 416 ASN B 415 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8685 Z= 0.156 Angle : 0.513 7.721 11790 Z= 0.246 Chirality : 0.039 0.133 1356 Planarity : 0.005 0.050 1383 Dihedral : 14.608 126.844 1566 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.85 % Allowed : 11.69 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.27), residues: 1050 helix: 1.01 (0.19), residues: 753 sheet: None (None), residues: 0 loop : 0.15 (0.41), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 108 HIS 0.002 0.000 HIS B 319 PHE 0.021 0.001 PHE C 378 TYR 0.009 0.001 TYR A 184 ARG 0.001 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 0.896 Fit side-chains REVERT: A 119 ILE cc_start: 0.8378 (mt) cc_final: 0.7959 (mp) REVERT: A 387 SER cc_start: 0.8236 (OUTLIER) cc_final: 0.7979 (m) REVERT: C 119 ILE cc_start: 0.8353 (mt) cc_final: 0.7953 (mp) REVERT: B 408 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8107 (mt) outliers start: 15 outliers final: 6 residues processed: 106 average time/residue: 0.7261 time to fit residues: 85.3518 Evaluate side-chains 99 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 408 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.3848 > 50: distance: 86 - 90: 27.345 distance: 90 - 91: 9.069 distance: 91 - 92: 13.670 distance: 92 - 99: 12.932 distance: 94 - 95: 24.576 distance: 95 - 96: 27.817 distance: 96 - 97: 43.248 distance: 97 - 98: 18.872 distance: 99 - 100: 8.321 distance: 100 - 101: 23.133 distance: 100 - 103: 35.246 distance: 103 - 104: 16.058 distance: 104 - 105: 17.399 distance: 104 - 106: 19.087 distance: 105 - 107: 20.574 distance: 106 - 108: 17.735 distance: 106 - 109: 10.875 distance: 107 - 108: 13.948 distance: 108 - 110: 25.175 distance: 109 - 111: 14.676 distance: 110 - 112: 15.722 distance: 111 - 112: 16.265 distance: 113 - 114: 25.273 distance: 114 - 115: 24.006 distance: 114 - 117: 28.543 distance: 115 - 116: 20.506 distance: 115 - 121: 10.513 distance: 117 - 118: 49.771 distance: 118 - 119: 9.072 distance: 118 - 120: 3.136 distance: 121 - 122: 15.052 distance: 122 - 123: 26.359 distance: 122 - 125: 12.916 distance: 123 - 124: 31.574 distance: 123 - 129: 29.330 distance: 125 - 126: 26.798 distance: 126 - 127: 38.341 distance: 126 - 128: 41.497 distance: 129 - 130: 28.780 distance: 129 - 135: 36.037 distance: 130 - 131: 26.504 distance: 130 - 133: 9.425 distance: 131 - 132: 25.406 distance: 131 - 136: 14.670 distance: 133 - 134: 19.656 distance: 134 - 135: 23.057 distance: 136 - 137: 22.604 distance: 137 - 138: 19.057 distance: 137 - 140: 6.440 distance: 138 - 139: 23.956 distance: 138 - 143: 27.260 distance: 140 - 141: 17.639 distance: 140 - 142: 29.856 distance: 143 - 144: 13.477 distance: 144 - 145: 11.271 distance: 144 - 147: 10.029 distance: 145 - 146: 17.733 distance: 145 - 154: 12.353 distance: 147 - 148: 15.882 distance: 148 - 149: 12.462 distance: 148 - 150: 16.096 distance: 149 - 151: 18.537 distance: 150 - 152: 13.092 distance: 151 - 153: 15.903 distance: 152 - 153: 10.912 distance: 154 - 155: 28.749 distance: 155 - 156: 27.818 distance: 155 - 158: 8.641 distance: 156 - 157: 19.357 distance: 158 - 159: 43.236 distance: 158 - 160: 17.310 distance: 161 - 162: 25.140 distance: 162 - 163: 26.278 distance: 162 - 165: 24.548 distance: 163 - 164: 6.898 distance: 163 - 169: 12.744 distance: 164 - 192: 25.796 distance: 165 - 166: 21.964 distance: 166 - 167: 18.901 distance: 166 - 168: 25.057 distance: 169 - 170: 7.822 distance: 169 - 175: 5.729 distance: 170 - 171: 16.145 distance: 171 - 172: 3.672 distance: 171 - 176: 21.302 distance: 172 - 199: 18.820 distance: 173 - 174: 9.626 distance: 174 - 175: 8.341