Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 22:10:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/10_2023/7wf7_32461_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/10_2023/7wf7_32461.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/10_2023/7wf7_32461_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/10_2023/7wf7_32461_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/10_2023/7wf7_32461_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/10_2023/7wf7_32461.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/10_2023/7wf7_32461.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/10_2023/7wf7_32461_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/10_2023/7wf7_32461_neut_updated.pdb" } resolution = 3.4 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= 0.113 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 1 5.49 5 S 56 5.16 5 C 5207 2.51 5 N 1380 2.21 5 O 1492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 8136 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2189 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 6, 'TRANS': 264} Chain breaks: 5 Chain: "B" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1143 Classifications: {'peptide': 142} Link IDs: {'TRANS': 141} Chain breaks: 5 Chain: "C" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "D" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 410 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'S1P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.84, per 1000 atoms: 0.59 Number of scatterers: 8136 At special positions: 0 Unit cell: (92.4, 124.3, 132, 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 56 16.00 P 1 15.00 O 1492 8.00 N 1380 7.00 C 5207 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 191 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.05 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: 3.06 Conformation dependent library (CDL) restraints added in 1.3 seconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1932 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 13 sheets defined 31.4% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 47 through 71 Processing helix chain 'A' and resid 79 through 103 Processing helix chain 'A' and resid 107 through 110 Processing helix chain 'A' and resid 114 through 145 Processing helix chain 'A' and resid 159 through 180 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 202 through 233 Processing helix chain 'A' and resid 255 through 279 removed outlier: 5.200A pdb=" N ILE A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) Proline residue: A 271 - end of helix removed outlier: 3.757A pdb=" N LEU A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 291 Processing helix chain 'A' and resid 297 through 305 removed outlier: 4.134A pdb=" N SER A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 310 No H-bonds generated for 'chain 'A' and resid 307 through 310' Processing helix chain 'A' and resid 316 through 323 Processing helix chain 'B' and resid 7 through 32 removed outlier: 4.009A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 52 removed outlier: 4.008A pdb=" N LYS B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 removed outlier: 3.822A pdb=" N GLU B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 350 removed outlier: 4.588A pdb=" N PHE B 334 " --> pdb=" O ASN B 331 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LYS B 345 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 23 Processing helix chain 'C' and resid 30 through 36 removed outlier: 5.090A pdb=" N ASN C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 264 through 266 removed outlier: 6.264A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.936A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.162A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.838A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 220 through 223 removed outlier: 4.283A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 200 " --> pdb=" O SER C 191 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER C 189 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.573A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 305 through 307 removed outlier: 4.009A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 47 through 51 removed outlier: 7.090A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.316A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 128 through 130 Processing sheet with id= L, first strand: chain 'E' and resid 134 through 136 removed outlier: 7.228A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 213 through 219 removed outlier: 6.291A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 361 hydrogen bonds defined for protein. 981 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: 2.40 Time building geometry restraints manager: 3.34 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: 2565 1.34 - 1.46: 1956 1.46 - 1.58: 3686 1.58 - 1.70: 6 1.70 - 1.83: 81 Bond restraints: 8294 Sorted by residual: bond pdb=" O1 S1P A 401 " pdb=" P22 S1P A 401 " ideal model delta sigma weight residual 1.661 1.815 -0.154 2.00e-02 2.50e+03 5.94e+01 bond pdb=" C5 S1P A 401 " pdb=" C6 S1P A 401 " ideal model delta sigma weight residual 1.550 1.486 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C13 S1P A 401 " pdb=" C14 S1P A 401 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.11e+00 bond pdb=" C6 S1P A 401 " pdb=" C7 S1P A 401 " ideal model delta sigma weight residual 1.554 1.606 -0.052 2.00e-02 2.50e+03 6.84e+00 bond pdb=" C15 S1P A 401 " pdb=" C16 S1P A 401 " ideal model delta sigma weight residual 1.561 1.510 0.051 2.00e-02 2.50e+03 6.61e+00 ... (remaining 8289 not shown) Histogram of bond angle deviations from ideal: 95.09 - 102.88: 40 102.88 - 110.67: 2514 110.67 - 118.46: 3901 118.46 - 126.25: 4634 126.25 - 134.04: 128 Bond angle restraints: 11217 Sorted by residual: angle pdb=" O1 S1P A 401 " pdb=" P22 S1P A 401 " pdb=" O25 S1P A 401 " ideal model delta sigma weight residual 109.48 95.09 14.39 3.00e+00 1.11e-01 2.30e+01 angle pdb=" N PHE C 235 " pdb=" CA PHE C 235 " pdb=" C PHE C 235 " ideal model delta sigma weight residual 108.85 100.57 8.28 1.88e+00 2.83e-01 1.94e+01 angle pdb=" N TYR E 94 " pdb=" CA TYR E 94 " pdb=" C TYR E 94 " ideal model delta sigma weight residual 108.76 115.88 -7.12 1.69e+00 3.50e-01 1.78e+01 angle pdb=" C PHE C 235 " pdb=" CA PHE C 235 " pdb=" CB PHE C 235 " ideal model delta sigma weight residual 110.13 115.24 -5.11 1.34e+00 5.57e-01 1.46e+01 angle pdb=" C LEU C 70 " pdb=" CA LEU C 70 " pdb=" CB LEU C 70 " ideal model delta sigma weight residual 109.65 103.02 6.63 1.75e+00 3.27e-01 1.44e+01 ... (remaining 11212 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.76: 4715 26.76 - 53.52: 170 53.52 - 80.28: 12 80.28 - 107.04: 2 107.04 - 133.80: 2 Dihedral angle restraints: 4901 sinusoidal: 1914 harmonic: 2987 Sorted by residual: dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 133.38 -40.38 1 1.00e+01 1.00e-02 2.29e+01 dihedral pdb=" C10 S1P A 401 " pdb=" C11 S1P A 401 " pdb=" C12 S1P A 401 " pdb=" C13 S1P A 401 " ideal model delta sinusoidal sigma weight residual 222.74 88.94 133.80 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" CA ASN C 293 " pdb=" C ASN C 293 " pdb=" N CYS C 294 " pdb=" CA CYS C 294 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 4898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 942 0.045 - 0.090: 263 0.090 - 0.136: 83 0.136 - 0.181: 6 0.181 - 0.226: 4 Chirality restraints: 1298 Sorted by residual: chirality pdb=" CA ASP C 247 " pdb=" N ASP C 247 " pdb=" C ASP C 247 " pdb=" CB ASP C 247 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C3 S1P A 401 " pdb=" C2 S1P A 401 " pdb=" C4 S1P A 401 " pdb=" O3 S1P A 401 " both_signs ideal model delta sigma weight residual False -2.52 -2.32 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA LYS A 256 " pdb=" N LYS A 256 " pdb=" C LYS A 256 " pdb=" CB LYS A 256 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1295 not shown) Planarity restraints: 1388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 169 " -0.026 2.00e-02 2.50e+03 1.89e-02 8.94e+00 pdb=" CG TRP C 169 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP C 169 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP C 169 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 169 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 169 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 106 " -0.042 5.00e-02 4.00e+02 6.51e-02 6.77e+00 pdb=" N PRO E 107 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO E 107 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 107 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 307 " 0.034 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO A 308 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 308 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 308 " 0.029 5.00e-02 4.00e+02 ... (remaining 1385 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2248 2.81 - 3.33: 7374 3.33 - 3.86: 12724 3.86 - 4.38: 14790 4.38 - 4.90: 25716 Nonbonded interactions: 62852 Sorted by model distance: nonbonded pdb=" OG1 THR C 143 " pdb=" OD1 ASP C 163 " model vdw 2.288 2.440 nonbonded pdb=" N GLY C 144 " pdb=" OD1 ASP C 163 " model vdw 2.295 2.520 nonbonded pdb=" O ARG C 314 " pdb=" OG SER C 331 " model vdw 2.297 2.440 nonbonded pdb=" OG1 THR C 34 " pdb=" O LEU C 300 " model vdw 2.320 2.440 nonbonded pdb=" O SER E 120 " pdb=" OG SER E 120 " model vdw 2.328 2.440 ... (remaining 62847 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.880 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: 3.940 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 24.740 Find NCS groups from input model: 0.190 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 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 0.154 8294 Z= 0.265 Angle : 0.835 14.386 11217 Z= 0.459 Chirality : 0.046 0.226 1298 Planarity : 0.005 0.065 1388 Dihedral : 13.559 133.800 2963 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.14 (0.26), residues: 1002 helix: 0.94 (0.30), residues: 297 sheet: -0.65 (0.30), residues: 266 loop : -2.04 (0.28), residues: 439 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2277 time to fit residues: 46.6091 Evaluate side-chains 100 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.924 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 101 ASN B 347 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8294 Z= 0.231 Angle : 0.664 8.818 11217 Z= 0.350 Chirality : 0.044 0.165 1298 Planarity : 0.005 0.049 1388 Dihedral : 7.313 121.056 1125 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.69 % Allowed : 8.66 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.69 (0.26), residues: 1002 helix: 1.60 (0.30), residues: 296 sheet: -0.47 (0.30), residues: 259 loop : -1.92 (0.28), residues: 447 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 0.847 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 109 average time/residue: 0.2424 time to fit residues: 35.3536 Evaluate side-chains 109 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.902 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0825 time to fit residues: 2.8054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.0570 chunk 28 optimal weight: 0.7980 chunk 77 optimal weight: 0.0000 chunk 63 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 91 optimal weight: 0.0770 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8294 Z= 0.206 Angle : 0.619 8.346 11217 Z= 0.327 Chirality : 0.042 0.160 1298 Planarity : 0.004 0.042 1388 Dihedral : 6.820 117.057 1125 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.24 % Allowed : 12.26 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.51 (0.26), residues: 1002 helix: 1.84 (0.30), residues: 296 sheet: -0.46 (0.30), residues: 249 loop : -1.80 (0.28), residues: 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 0.912 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 113 average time/residue: 0.2296 time to fit residues: 35.0443 Evaluate side-chains 107 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0768 time to fit residues: 1.9693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 44 optimal weight: 0.0070 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 0.0010 chunk 98 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5804 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8294 Z= 0.152 Angle : 0.555 8.859 11217 Z= 0.295 Chirality : 0.041 0.152 1298 Planarity : 0.004 0.041 1388 Dihedral : 6.244 102.677 1125 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.24 % Allowed : 13.50 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.17 (0.27), residues: 1002 helix: 2.07 (0.30), residues: 296 sheet: -0.19 (0.31), residues: 243 loop : -1.57 (0.28), residues: 463 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 0.801 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 116 average time/residue: 0.2226 time to fit residues: 34.8940 Evaluate side-chains 108 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 0.816 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0733 time to fit residues: 1.9014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 84 optimal weight: 0.0870 chunk 68 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 0.0470 chunk 88 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 19 optimal weight: 0.0970 overall best weight: 0.3254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8294 Z= 0.123 Angle : 0.506 8.533 11217 Z= 0.268 Chirality : 0.040 0.144 1298 Planarity : 0.004 0.040 1388 Dihedral : 5.802 85.796 1125 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.57 % Allowed : 13.84 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.06 (0.27), residues: 1002 helix: 2.33 (0.31), residues: 294 sheet: -0.09 (0.31), residues: 248 loop : -1.46 (0.29), residues: 460 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 0.883 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 122 average time/residue: 0.2272 time to fit residues: 37.3304 Evaluate side-chains 111 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 0.897 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0817 time to fit residues: 2.7360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.2721 > 50: distance: 48 - 183: 3.063 distance: 56 - 62: 16.191 distance: 62 - 63: 25.389 distance: 62 - 173: 15.068 distance: 63 - 64: 29.073 distance: 63 - 66: 27.885 distance: 64 - 65: 33.543 distance: 64 - 76: 45.818 distance: 65 - 170: 20.545 distance: 66 - 67: 13.121 distance: 67 - 68: 13.928 distance: 67 - 69: 11.345 distance: 68 - 70: 9.957 distance: 69 - 71: 5.538 distance: 69 - 72: 7.053 distance: 70 - 71: 3.879 distance: 72 - 74: 6.709 distance: 73 - 75: 3.031 distance: 74 - 75: 6.002 distance: 76 - 77: 27.801 distance: 76 - 226: 37.997 distance: 77 - 78: 41.297 distance: 77 - 80: 33.382 distance: 78 - 79: 34.990 distance: 78 - 87: 38.469 distance: 79 - 223: 18.821 distance: 80 - 81: 18.007 distance: 81 - 82: 17.663 distance: 81 - 83: 18.652 distance: 82 - 84: 21.015 distance: 83 - 85: 12.172 distance: 84 - 86: 10.551 distance: 85 - 86: 4.830 distance: 87 - 88: 33.516 distance: 88 - 89: 27.139 distance: 88 - 91: 30.519 distance: 89 - 90: 24.598 distance: 89 - 95: 27.350 distance: 91 - 92: 21.268 distance: 92 - 93: 17.321 distance: 92 - 94: 19.248 distance: 95 - 96: 16.262 distance: 95 - 208: 29.717 distance: 96 - 97: 22.085 distance: 96 - 99: 18.190 distance: 97 - 98: 20.966 distance: 97 - 104: 18.786 distance: 98 - 205: 8.243 distance: 99 - 100: 14.209 distance: 100 - 101: 19.305 distance: 101 - 102: 9.631 distance: 101 - 103: 6.261 distance: 104 - 105: 27.722 distance: 105 - 106: 56.000 distance: 105 - 108: 25.416 distance: 106 - 107: 48.682 distance: 106 - 115: 58.203 distance: 108 - 109: 16.872 distance: 109 - 110: 11.336 distance: 110 - 111: 7.341 distance: 111 - 112: 4.688 distance: 112 - 113: 4.495 distance: 112 - 114: 3.242 distance: 115 - 116: 58.124 distance: 115 - 121: 47.149 distance: 116 - 117: 51.631 distance: 116 - 119: 47.672 distance: 117 - 118: 43.669 distance: 117 - 122: 50.290 distance: 119 - 120: 15.278 distance: 120 - 121: 23.600 distance: 122 - 123: 22.768 distance: 123 - 124: 25.765 distance: 124 - 125: 28.674 distance: 124 - 126: 18.456 distance: 126 - 127: 9.453 distance: 127 - 128: 34.324 distance: 127 - 130: 21.403 distance: 128 - 129: 35.173 distance: 128 - 135: 10.275 distance: 130 - 131: 24.544 distance: 131 - 132: 4.930 distance: 132 - 133: 7.919 distance: 132 - 134: 20.508 distance: 135 - 136: 7.074 distance: 136 - 137: 35.362 distance: 136 - 139: 27.645 distance: 137 - 138: 33.037 distance: 137 - 141: 19.584 distance: 139 - 140: 40.483 distance: 141 - 142: 10.770 distance: 141 - 147: 19.957 distance: 142 - 143: 40.248 distance: 142 - 145: 24.829 distance: 143 - 144: 41.230 distance: 143 - 148: 28.399 distance: 145 - 146: 20.573 distance: 146 - 147: 21.489