Starting phenix.real_space_refine on Thu Jan 18 08:07:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7agg_11779/01_2024/7agg_11779.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7agg_11779/01_2024/7agg_11779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7agg_11779/01_2024/7agg_11779.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7agg_11779/01_2024/7agg_11779.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7agg_11779/01_2024/7agg_11779.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7agg_11779/01_2024/7agg_11779.pdb" } resolution = 3.3 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= 0.000 sd= 0.001 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 33 5.16 5 C 5206 2.51 5 N 1344 2.21 5 O 1669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 196": "OE1" <-> "OE2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D GLU 240": "OE1" <-> "OE2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 268": "OE1" <-> "OE2" Residue "D TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 300": "OD1" <-> "OD2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 323": "OE1" <-> "OE2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 323": "OE1" <-> "OE2" Residue "F GLU 155": "OE1" <-> "OE2" Residue "F TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 198": "OE1" <-> "OE2" Residue "F GLU 240": "OE1" <-> "OE2" Residue "F PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 268": "OE1" <-> "OE2" Residue "F TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 300": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 8252 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1538 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "D" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1819 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain: "B" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1538 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "C" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1538 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "F" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1819 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Time building chain proxies: 4.81, per 1000 atoms: 0.58 Number of scatterers: 8252 At special positions: 0 Unit cell: (113.75, 110.5, 101.4, 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 33 16.00 O 1669 8.00 N 1344 7.00 C 5206 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: 2.89 Conformation dependent library (CDL) restraints added in 1.5 seconds 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2018 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 17 sheets defined 7.5% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.558A pdb=" N GLY A 234 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 252 removed outlier: 5.642A pdb=" N LYS A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 252 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 296 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 185 through 188 Processing helix chain 'B' and resid 231 through 236 removed outlier: 3.558A pdb=" N GLY B 234 " --> pdb=" O ASN B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 252 removed outlier: 5.642A pdb=" N LYS B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU B 252 " --> pdb=" O ARG B 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 185 through 188 Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.557A pdb=" N GLY C 234 " --> pdb=" O ASN C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 252 removed outlier: 5.642A pdb=" N LYS C 251 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU C 252 " --> pdb=" O ARG C 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 296 Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 135 removed outlier: 3.573A pdb=" N TYR A 320 " --> pdb=" O VAL A 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 199 removed outlier: 5.896A pdb=" N ASN A 297 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 220 Processing sheet with id=AA4, first strand: chain 'D' and resid 114 through 120 removed outlier: 6.990A pdb=" N THR D 187 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU D 154 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR D 189 " --> pdb=" O VAL D 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 130 through 131 removed outlier: 3.579A pdb=" N MET D 130 " --> pdb=" O ILE D 171 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 222 through 223 Processing sheet with id=AA7, first strand: chain 'D' and resid 229 through 231 removed outlier: 6.723A pdb=" N SER D 302 " --> pdb=" O ALA D 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 133 through 135 removed outlier: 3.573A pdb=" N TYR B 320 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 190 through 199 removed outlier: 5.896A pdb=" N ASN B 297 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 219 through 220 Processing sheet with id=AB2, first strand: chain 'C' and resid 133 through 135 removed outlier: 3.572A pdb=" N TYR C 320 " --> pdb=" O VAL C 169 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 190 through 199 removed outlier: 5.897A pdb=" N ASN C 297 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 219 through 220 Processing sheet with id=AB5, first strand: chain 'F' and resid 114 through 120 removed outlier: 6.991A pdb=" N THR F 187 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU F 154 " --> pdb=" O THR F 187 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR F 189 " --> pdb=" O VAL F 152 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 130 through 131 removed outlier: 3.578A pdb=" N MET F 130 " --> pdb=" O ILE F 171 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 222 through 223 Processing sheet with id=AB8, first strand: chain 'F' and resid 229 through 231 removed outlier: 6.725A pdb=" N SER F 302 " --> pdb=" O ALA F 264 " (cutoff:3.500A) 220 hydrogen bonds defined for protein. 537 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: 2.11 Time building geometry restraints manager: 3.16 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: 2700 1.34 - 1.46: 1662 1.46 - 1.57: 4002 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 8418 Sorted by residual: bond pdb=" CB TRP C 135 " pdb=" CG TRP C 135 " ideal model delta sigma weight residual 1.498 1.443 0.055 3.10e-02 1.04e+03 3.10e+00 bond pdb=" CB TRP A 135 " pdb=" CG TRP A 135 " ideal model delta sigma weight residual 1.498 1.444 0.054 3.10e-02 1.04e+03 3.06e+00 bond pdb=" CB TRP B 135 " pdb=" CG TRP B 135 " ideal model delta sigma weight residual 1.498 1.444 0.054 3.10e-02 1.04e+03 3.03e+00 bond pdb=" CG1 ILE B 273 " pdb=" CD1 ILE B 273 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.09e+00 bond pdb=" CG1 ILE A 273 " pdb=" CD1 ILE A 273 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.08e+00 ... (remaining 8413 not shown) Histogram of bond angle deviations from ideal: 98.89 - 105.92: 169 105.92 - 112.95: 4640 112.95 - 119.97: 2729 119.97 - 127.00: 3867 127.00 - 134.02: 85 Bond angle restraints: 11490 Sorted by residual: angle pdb=" N TRP A 135 " pdb=" CA TRP A 135 " pdb=" CB TRP A 135 " ideal model delta sigma weight residual 111.56 106.66 4.90 1.52e+00 4.33e-01 1.04e+01 angle pdb=" N TRP C 135 " pdb=" CA TRP C 135 " pdb=" CB TRP C 135 " ideal model delta sigma weight residual 111.56 106.66 4.90 1.52e+00 4.33e-01 1.04e+01 angle pdb=" N TRP B 135 " pdb=" CA TRP B 135 " pdb=" CB TRP B 135 " ideal model delta sigma weight residual 111.56 106.68 4.88 1.52e+00 4.33e-01 1.03e+01 angle pdb=" C LYS D 313 " pdb=" CA LYS D 313 " pdb=" CB LYS D 313 " ideal model delta sigma weight residual 110.96 106.03 4.93 1.54e+00 4.22e-01 1.03e+01 angle pdb=" C LYS F 313 " pdb=" CA LYS F 313 " pdb=" CB LYS F 313 " ideal model delta sigma weight residual 110.96 106.03 4.93 1.54e+00 4.22e-01 1.02e+01 ... (remaining 11485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 4637 17.28 - 34.56: 311 34.56 - 51.85: 44 51.85 - 69.13: 19 69.13 - 86.41: 8 Dihedral angle restraints: 5019 sinusoidal: 1907 harmonic: 3112 Sorted by residual: dihedral pdb=" CA GLU D 240 " pdb=" C GLU D 240 " pdb=" N VAL D 241 " pdb=" CA VAL D 241 " ideal model delta harmonic sigma weight residual 180.00 -154.69 -25.31 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA GLU F 240 " pdb=" C GLU F 240 " pdb=" N VAL F 241 " pdb=" CA VAL F 241 " ideal model delta harmonic sigma weight residual -180.00 -154.72 -25.28 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ILE F 315 " pdb=" C ILE F 315 " pdb=" N ARG F 316 " pdb=" CA ARG F 316 " ideal model delta harmonic sigma weight residual 180.00 155.57 24.43 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 5016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1024 0.057 - 0.115: 292 0.115 - 0.172: 39 0.172 - 0.230: 0 0.230 - 0.287: 2 Chirality restraints: 1357 Sorted by residual: chirality pdb=" CB VAL D 204 " pdb=" CA VAL D 204 " pdb=" CG1 VAL D 204 " pdb=" CG2 VAL D 204 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB VAL F 204 " pdb=" CA VAL F 204 " pdb=" CG1 VAL F 204 " pdb=" CG2 VAL F 204 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA TYR F 158 " pdb=" N TYR F 158 " pdb=" C TYR F 158 " pdb=" CB TYR F 158 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.49e-01 ... (remaining 1354 not shown) Planarity restraints: 1484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 135 " -0.040 2.00e-02 2.50e+03 4.40e-02 4.83e+01 pdb=" CG TRP A 135 " 0.113 2.00e-02 2.50e+03 pdb=" CD1 TRP A 135 " -0.067 2.00e-02 2.50e+03 pdb=" CD2 TRP A 135 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 135 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 135 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 135 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 135 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 135 " -0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP A 135 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 135 " -0.040 2.00e-02 2.50e+03 4.39e-02 4.82e+01 pdb=" CG TRP C 135 " 0.113 2.00e-02 2.50e+03 pdb=" CD1 TRP C 135 " -0.067 2.00e-02 2.50e+03 pdb=" CD2 TRP C 135 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP C 135 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP C 135 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP C 135 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 135 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 135 " -0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP C 135 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 135 " 0.040 2.00e-02 2.50e+03 4.39e-02 4.81e+01 pdb=" CG TRP B 135 " -0.113 2.00e-02 2.50e+03 pdb=" CD1 TRP B 135 " 0.067 2.00e-02 2.50e+03 pdb=" CD2 TRP B 135 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 135 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 135 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 135 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 135 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 135 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP B 135 " 0.002 2.00e-02 2.50e+03 ... (remaining 1481 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 74 2.56 - 3.15: 6661 3.15 - 3.73: 12795 3.73 - 4.32: 18999 4.32 - 4.90: 30816 Nonbonded interactions: 69345 Sorted by model distance: nonbonded pdb=" OH TYR A 319 " pdb=" OH TYR B 319 " model vdw 1.980 2.440 nonbonded pdb=" O HIS F 273 " pdb=" OG1 THR F 286 " model vdw 2.236 2.440 nonbonded pdb=" O HIS D 273 " pdb=" OG1 THR D 286 " model vdw 2.237 2.440 nonbonded pdb=" OG SER A 238 " pdb=" OE1 GLN B 222 " model vdw 2.241 2.440 nonbonded pdb=" OG1 THR B 165 " pdb=" OG1 THR B 170 " model vdw 2.292 2.440 ... (remaining 69340 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' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 2.220 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: 7.100 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 24.350 Find NCS groups from input model: 0.550 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: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 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 0.056 8418 Z= 0.463 Angle : 0.785 6.289 11490 Z= 0.455 Chirality : 0.052 0.287 1357 Planarity : 0.005 0.050 1484 Dihedral : 13.158 86.411 3001 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -1.18 (0.26), residues: 1046 helix: -2.40 (0.61), residues: 54 sheet: -0.53 (0.26), residues: 370 loop : -0.73 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.113 0.010 TRP A 135 HIS 0.007 0.002 HIS F 312 PHE 0.016 0.002 PHE B 199 TYR 0.038 0.003 TYR F 293 ARG 0.008 0.002 ARG C 280 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 174 THR cc_start: 0.8912 (p) cc_final: 0.8559 (t) REVERT: B 156 CYS cc_start: 0.6660 (p) cc_final: 0.6230 (p) REVERT: F 189 THR cc_start: 0.7935 (m) cc_final: 0.7224 (p) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2255 time to fit residues: 66.8628 Evaluate side-chains 147 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 0.0770 chunk 26 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 93 optimal weight: 0.0000 overall best weight: 0.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN D 206 GLN D 208 GLN ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 GLN ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8418 Z= 0.139 Angle : 0.529 5.714 11490 Z= 0.286 Chirality : 0.045 0.172 1357 Planarity : 0.004 0.050 1484 Dihedral : 5.342 22.276 1121 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.43 % Allowed : 9.58 % Favored : 89.99 % 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: -0.70 (0.26), residues: 1046 helix: -1.40 (0.84), residues: 36 sheet: -0.12 (0.27), residues: 370 loop : -0.57 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP B 135 HIS 0.002 0.000 HIS D 273 PHE 0.015 0.002 PHE F 115 TYR 0.020 0.001 TYR D 293 ARG 0.006 0.001 ARG F 212 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 172 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 174 THR cc_start: 0.8817 (p) cc_final: 0.8597 (t) REVERT: F 150 ARG cc_start: 0.7283 (ptt180) cc_final: 0.6001 (ptt180) REVERT: F 189 THR cc_start: 0.7552 (m) cc_final: 0.6954 (p) REVERT: F 300 ASP cc_start: 0.8017 (t0) cc_final: 0.7255 (p0) outliers start: 4 outliers final: 4 residues processed: 173 average time/residue: 0.2212 time to fit residues: 51.7687 Evaluate side-chains 146 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain B residue 191 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 208 GLN ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN B 188 HIS C 188 HIS ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 219 ASN F 236 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 8418 Z= 0.472 Angle : 0.681 7.065 11490 Z= 0.368 Chirality : 0.048 0.156 1357 Planarity : 0.005 0.070 1484 Dihedral : 5.933 27.234 1121 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.88 % Allowed : 11.18 % Favored : 85.94 % 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: -0.96 (0.26), residues: 1046 helix: -0.56 (1.10), residues: 21 sheet: -0.49 (0.26), residues: 376 loop : -0.69 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.005 TRP C 135 HIS 0.008 0.001 HIS F 183 PHE 0.014 0.002 PHE D 301 TYR 0.023 0.002 TYR F 293 ARG 0.004 0.001 ARG F 212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 150 time to evaluate : 1.086 Fit side-chains REVERT: C 196 GLU cc_start: 0.6512 (mm-30) cc_final: 0.5071 (mm-30) REVERT: C 303 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7285 (mm-30) REVERT: F 189 THR cc_start: 0.7858 (m) cc_final: 0.7300 (p) REVERT: F 293 TYR cc_start: 0.4260 (p90) cc_final: 0.4013 (p90) REVERT: F 301 PHE cc_start: 0.8040 (p90) cc_final: 0.7661 (p90) REVERT: F 304 ILE cc_start: 0.9138 (mm) cc_final: 0.8918 (mt) outliers start: 27 outliers final: 21 residues processed: 167 average time/residue: 0.2181 time to fit residues: 49.2542 Evaluate side-chains 154 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 TRP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain F residue 315 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 62 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 217 ASN F 106 ASN F 236 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8418 Z= 0.188 Angle : 0.528 6.778 11490 Z= 0.283 Chirality : 0.044 0.149 1357 Planarity : 0.004 0.056 1484 Dihedral : 5.131 22.400 1121 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.45 % Allowed : 13.74 % Favored : 83.81 % 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: -0.86 (0.26), residues: 1046 helix: -0.39 (1.15), residues: 21 sheet: -0.44 (0.26), residues: 376 loop : -0.61 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 135 HIS 0.002 0.000 HIS F 183 PHE 0.011 0.002 PHE A 172 TYR 0.016 0.001 TYR D 293 ARG 0.005 0.001 ARG F 193 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 1.118 Fit side-chains REVERT: B 128 ASP cc_start: 0.7380 (t0) cc_final: 0.7155 (t0) REVERT: C 303 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7202 (mm-30) REVERT: F 139 GLU cc_start: 0.7778 (mp0) cc_final: 0.7480 (mp0) REVERT: F 189 THR cc_start: 0.7717 (m) cc_final: 0.7155 (p) REVERT: F 301 PHE cc_start: 0.7997 (p90) cc_final: 0.7675 (p90) REVERT: F 304 ILE cc_start: 0.9041 (mm) cc_final: 0.8806 (mt) outliers start: 23 outliers final: 13 residues processed: 162 average time/residue: 0.2118 time to fit residues: 46.4852 Evaluate side-chains 150 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 137 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 241 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 52.3199 > 50: distance: 36 - 196: 24.650 distance: 75 - 188: 23.605 distance: 78 - 185: 20.717 distance: 92 - 173: 8.276 distance: 95 - 170: 17.879 distance: 124 - 128: 19.797 distance: 128 - 129: 17.501 distance: 129 - 130: 9.876 distance: 129 - 132: 12.997 distance: 130 - 131: 24.758 distance: 130 - 140: 14.232 distance: 132 - 133: 19.901 distance: 133 - 134: 13.448 distance: 133 - 135: 13.664 distance: 134 - 136: 18.470 distance: 135 - 137: 17.618 distance: 136 - 138: 14.565 distance: 137 - 138: 4.066 distance: 138 - 139: 3.795 distance: 140 - 141: 26.139 distance: 141 - 142: 46.283 distance: 141 - 144: 24.131 distance: 142 - 143: 43.947 distance: 142 - 149: 52.320 distance: 144 - 145: 17.732 distance: 145 - 146: 8.121 distance: 146 - 147: 17.800 distance: 147 - 148: 13.516 distance: 149 - 150: 26.522 distance: 149 - 155: 29.826 distance: 150 - 151: 44.955 distance: 150 - 153: 41.051 distance: 151 - 152: 16.956 distance: 151 - 156: 15.437 distance: 153 - 154: 12.223 distance: 154 - 155: 15.799 distance: 156 - 157: 14.585 distance: 157 - 158: 14.729 distance: 157 - 160: 25.781 distance: 158 - 159: 45.869 distance: 158 - 163: 30.305 distance: 160 - 161: 26.003 distance: 160 - 162: 34.261 distance: 163 - 164: 16.539 distance: 163 - 169: 40.798 distance: 164 - 165: 15.625 distance: 164 - 167: 30.628 distance: 165 - 166: 29.391 distance: 165 - 170: 13.720 distance: 167 - 168: 16.745 distance: 168 - 169: 36.143 distance: 170 - 171: 34.461 distance: 171 - 172: 9.305 distance: 171 - 174: 21.490 distance: 172 - 173: 17.271 distance: 172 - 178: 37.660 distance: 174 - 175: 37.584 distance: 174 - 176: 22.208 distance: 175 - 177: 27.494 distance: 178 - 179: 31.028 distance: 178 - 184: 31.191 distance: 179 - 180: 50.844 distance: 179 - 182: 50.818 distance: 180 - 181: 23.679 distance: 180 - 185: 32.302 distance: 182 - 183: 10.230 distance: 183 - 184: 29.994 distance: 185 - 186: 7.374 distance: 186 - 187: 25.600 distance: 186 - 189: 28.309 distance: 187 - 188: 25.521 distance: 187 - 193: 12.891 distance: 189 - 190: 29.810 distance: 189 - 191: 20.242 distance: 190 - 192: 34.464 distance: 193 - 194: 41.379 distance: 194 - 195: 40.336 distance: 194 - 197: 13.132 distance: 195 - 196: 38.642 distance: 195 - 202: 22.527 distance: 197 - 198: 37.063 distance: 198 - 199: 19.569 distance: 199 - 200: 19.366 distance: 200 - 201: 6.538 distance: 202 - 203: 9.143 distance: 203 - 204: 30.703 distance: 203 - 206: 39.137 distance: 204 - 205: 9.845 distance: 204 - 209: 18.571 distance: 206 - 207: 23.059 distance: 206 - 208: 19.030