Starting phenix.real_space_refine on Sat Aug 3 23:09:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3q_41008/08_2024/8t3q_41008.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3q_41008/08_2024/8t3q_41008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3q_41008/08_2024/8t3q_41008.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3q_41008/08_2024/8t3q_41008.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3q_41008/08_2024/8t3q_41008.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3q_41008/08_2024/8t3q_41008.cif" } resolution = 3.14 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= 0.034 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 55 5.16 5 C 5752 2.51 5 N 1562 2.21 5 O 1666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 151": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "N GLU 223": "OE1" <-> "OE2" Residue "N GLU 235": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "R ARG 22": "NH1" <-> "NH2" Residue "R ARG 24": "NH1" <-> "NH2" Residue "R PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 99": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9035 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1800 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "N" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1781 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2372 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain breaks: 2 Chain: "R" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'HXA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.58, per 1000 atoms: 0.62 Number of scatterers: 9035 At special positions: 0 Unit cell: (85.284, 124.2, 125.856, 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 55 16.00 O 1666 8.00 N 1562 7.00 C 5752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 160 " - pdb=" SG CYS N 230 " distance=2.03 Simple disulfide: pdb=" SG CYS R 111 " - pdb=" SG CYS R 194 " distance=2.03 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: 3.44 Conformation dependent library (CDL) restraints added in 1.6 seconds 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 15 sheets defined 36.6% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.232A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.724A pdb=" N ILE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.759A pdb=" N GLN A 98 " --> pdb=" O LYS A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.953A pdb=" N GLY A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 170 Processing helix chain 'A' and resid 183 through 204 removed outlier: 4.106A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 243 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.949A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 53 through 56 removed outlier: 3.532A pdb=" N GLY N 56 " --> pdb=" O SER N 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 53 through 56' Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.751A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 35 through 71 removed outlier: 3.568A pdb=" N VAL R 63 " --> pdb=" O VAL R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 89 Processing helix chain 'R' and resid 91 through 102 removed outlier: 3.653A pdb=" N THR R 101 " --> pdb=" O ALA R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 140 removed outlier: 3.539A pdb=" N LEU R 113 " --> pdb=" O VAL R 109 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE R 115 " --> pdb=" O CYS R 111 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR R 119 " --> pdb=" O PHE R 115 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER R 123 " --> pdb=" O THR R 119 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU R 127 " --> pdb=" O SER R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 170 Processing helix chain 'R' and resid 171 through 176 Processing helix chain 'R' and resid 200 through 216 Processing helix chain 'R' and resid 216 through 245 removed outlier: 3.675A pdb=" N GLY R 220 " --> pdb=" O PHE R 216 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU R 231 " --> pdb=" O TYR R 227 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR R 234 " --> pdb=" O ILE R 230 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU R 245 " --> pdb=" O LEU R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 256 Processing helix chain 'R' and resid 258 through 291 Proline residue: R 279 - end of helix Processing helix chain 'R' and resid 299 through 322 removed outlier: 3.824A pdb=" N SER R 314 " --> pdb=" O THR R 310 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA R 315 " --> pdb=" O PHE R 311 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU R 316 " --> pdb=" O ALA R 312 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 3.773A pdb=" N VAL A 109 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.312A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.860A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 5.924A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.973A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.920A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.711A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.687A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain 'N' and resid 58 through 60 removed outlier: 4.952A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 141 through 142 Processing sheet with id=AB5, first strand: chain 'N' and resid 148 through 149 removed outlier: 3.788A pdb=" N VAL N 148 " --> pdb=" O LYS N 245 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU N 247 " --> pdb=" O VAL N 148 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU N 175 " --> pdb=" O TYR N 191 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR N 191 " --> pdb=" O LEU N 175 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP N 177 " --> pdb=" O LEU N 189 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 180 through 181 445 hydrogen bonds defined for protein. 1254 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: 2.80 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1476 1.32 - 1.44: 2522 1.44 - 1.57: 5141 1.57 - 1.69: 0 1.69 - 1.81: 79 Bond restraints: 9218 Sorted by residual: bond pdb=" C HIS R 112 " pdb=" O HIS R 112 " ideal model delta sigma weight residual 1.236 1.313 -0.076 1.15e-02 7.56e+03 4.42e+01 bond pdb=" N VAL R 124 " pdb=" CA VAL R 124 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.08e-02 8.57e+03 1.35e+01 bond pdb=" N VAL R 117 " pdb=" CA VAL R 117 " ideal model delta sigma weight residual 1.460 1.501 -0.041 1.19e-02 7.06e+03 1.20e+01 bond pdb=" N VAL B 112 " pdb=" CA VAL B 112 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.11e-02 8.12e+03 1.19e+01 bond pdb=" C PRO R 108 " pdb=" O PRO R 108 " ideal model delta sigma weight residual 1.237 1.195 0.043 1.26e-02 6.30e+03 1.14e+01 ... (remaining 9213 not shown) Histogram of bond angle deviations from ideal: 98.94 - 106.04: 183 106.04 - 113.15: 4973 113.15 - 120.26: 3786 120.26 - 127.37: 3473 127.37 - 134.47: 87 Bond angle restraints: 12502 Sorted by residual: angle pdb=" N PRO N 237 " pdb=" CA PRO N 237 " pdb=" C PRO N 237 " ideal model delta sigma weight residual 110.95 99.26 11.69 1.62e+00 3.81e-01 5.21e+01 angle pdb=" N LEU R 120 " pdb=" CA LEU R 120 " pdb=" C LEU R 120 " ideal model delta sigma weight residual 113.12 105.33 7.79 1.25e+00 6.40e-01 3.88e+01 angle pdb=" N GLN R 290 " pdb=" CA GLN R 290 " pdb=" C GLN R 290 " ideal model delta sigma weight residual 112.23 104.42 7.81 1.26e+00 6.30e-01 3.84e+01 angle pdb=" N VAL R 124 " pdb=" CA VAL R 124 " pdb=" C VAL R 124 " ideal model delta sigma weight residual 113.42 106.79 6.63 1.17e+00 7.31e-01 3.21e+01 angle pdb=" C PHE B 151 " pdb=" CA PHE B 151 " pdb=" CB PHE B 151 " ideal model delta sigma weight residual 109.80 100.71 9.09 1.64e+00 3.72e-01 3.07e+01 ... (remaining 12497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 4884 17.15 - 34.31: 438 34.31 - 51.46: 125 51.46 - 68.62: 23 68.62 - 85.77: 7 Dihedral angle restraints: 5477 sinusoidal: 2119 harmonic: 3358 Sorted by residual: dihedral pdb=" CB CYS R 111 " pdb=" SG CYS R 111 " pdb=" SG CYS R 194 " pdb=" CB CYS R 194 " ideal model delta sinusoidal sigma weight residual 93.00 157.25 -64.25 1 1.00e+01 1.00e-02 5.43e+01 dihedral pdb=" C TYR N 236 " pdb=" N TYR N 236 " pdb=" CA TYR N 236 " pdb=" CB TYR N 236 " ideal model delta harmonic sigma weight residual -122.60 -136.52 13.92 0 2.50e+00 1.60e-01 3.10e+01 dihedral pdb=" N TYR N 236 " pdb=" C TYR N 236 " pdb=" CA TYR N 236 " pdb=" CB TYR N 236 " ideal model delta harmonic sigma weight residual 122.80 135.12 -12.32 0 2.50e+00 1.60e-01 2.43e+01 ... (remaining 5474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1197 0.100 - 0.200: 214 0.200 - 0.300: 25 0.300 - 0.401: 1 0.401 - 0.501: 1 Chirality restraints: 1438 Sorted by residual: chirality pdb=" CA TYR N 236 " pdb=" N TYR N 236 " pdb=" C TYR N 236 " pdb=" CB TYR N 236 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" CA LEU B 79 " pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CB LEU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA PHE B 151 " pdb=" N PHE B 151 " pdb=" C PHE B 151 " pdb=" CB PHE B 151 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1435 not shown) Planarity restraints: 1589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 HXA R 401 " 0.098 2.00e-02 2.50e+03 2.26e-01 5.11e+02 pdb=" C4 HXA R 401 " -0.301 2.00e-02 2.50e+03 pdb=" C5 HXA R 401 " 0.306 2.00e-02 2.50e+03 pdb=" C6 HXA R 401 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 HXA R 401 " -0.069 2.00e-02 2.50e+03 1.33e-01 1.77e+02 pdb=" C7 HXA R 401 " 0.175 2.00e-02 2.50e+03 pdb=" C8 HXA R 401 " -0.175 2.00e-02 2.50e+03 pdb=" C9 HXA R 401 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 HXA R 401 " 0.102 2.00e-02 2.50e+03 1.02e-01 1.04e+02 pdb=" C19 HXA R 401 " -0.101 2.00e-02 2.50e+03 pdb=" C20 HXA R 401 " -0.103 2.00e-02 2.50e+03 pdb=" C21 HXA R 401 " 0.102 2.00e-02 2.50e+03 ... (remaining 1586 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 323 2.69 - 3.25: 8908 3.25 - 3.80: 14332 3.80 - 4.35: 19120 4.35 - 4.90: 31430 Nonbonded interactions: 74113 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR N 176 " model vdw 2.144 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.144 3.040 nonbonded pdb=" OG SER N 157 " pdb=" OG1 THR N 214 " model vdw 2.221 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.292 3.040 nonbonded pdb=" NE2 HIS B 311 " pdb=" OG1 THR B 329 " model vdw 2.297 3.120 ... (remaining 74108 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.050 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 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 : 0.008 0.076 9218 Z= 0.532 Angle : 1.151 11.693 12502 Z= 0.813 Chirality : 0.074 0.501 1438 Planarity : 0.009 0.226 1589 Dihedral : 14.658 85.772 3294 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.29 % Favored : 95.62 % Rotamer: Outliers : 1.75 % Allowed : 16.63 % Favored : 81.62 % Cbeta Deviations : 0.18 % 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: -1.14 (0.25), residues: 1141 helix: -0.17 (0.27), residues: 375 sheet: -0.39 (0.32), residues: 270 loop : -1.33 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.009 0.002 HIS A 209 PHE 0.021 0.002 PHE B 151 TYR 0.032 0.002 TYR N 236 ARG 0.013 0.001 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.6652 (m-40) cc_final: 0.6419 (m-40) REVERT: B 197 ARG cc_start: 0.6821 (mmt180) cc_final: 0.6391 (mmt180) REVERT: B 214 ARG cc_start: 0.7733 (mpt180) cc_final: 0.7266 (ttp80) REVERT: B 217 MET cc_start: 0.6285 (mtt) cc_final: 0.5734 (ptp) REVERT: B 219 ARG cc_start: 0.6923 (mtt-85) cc_final: 0.6638 (mtp85) REVERT: N 235 GLU cc_start: 0.6954 (pt0) cc_final: 0.6604 (mt-10) REVERT: R 22 ARG cc_start: 0.4006 (mmp-170) cc_final: 0.2996 (mpp-170) REVERT: R 24 ARG cc_start: 0.6991 (mtp85) cc_final: 0.6574 (mtp180) REVERT: R 106 LEU cc_start: 0.8623 (mt) cc_final: 0.8415 (mt) REVERT: R 118 MET cc_start: 0.6056 (ttp) cc_final: 0.5672 (mtp) REVERT: R 215 ASN cc_start: 0.8202 (m-40) cc_final: 0.7360 (m-40) outliers start: 17 outliers final: 5 residues processed: 159 average time/residue: 0.2605 time to fit residues: 54.9575 Evaluate side-chains 133 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 118 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 8.9990 chunk 46 optimal weight: 0.5980 chunk 89 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS A 244 ASN B 9 GLN B 36 ASN B 44 GLN B 88 ASN R 112 HIS R 142 HIS R 182 GLN R 258 GLN R 290 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9218 Z= 0.192 Angle : 0.602 9.755 12502 Z= 0.318 Chirality : 0.043 0.167 1438 Planarity : 0.005 0.076 1589 Dihedral : 6.181 59.380 1280 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.77 % Allowed : 16.22 % Favored : 81.01 % 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: -0.57 (0.25), residues: 1141 helix: 0.57 (0.26), residues: 380 sheet: -0.19 (0.33), residues: 252 loop : -1.16 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 PHE 0.019 0.001 PHE R 27 TYR 0.014 0.001 TYR N 191 ARG 0.007 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.6450 (tttm) cc_final: 0.6163 (tttm) REVERT: A 199 ASP cc_start: 0.6201 (m-30) cc_final: 0.5991 (m-30) REVERT: A 238 MET cc_start: 0.6205 (ttm) cc_final: 0.6002 (ttm) REVERT: A 244 ASN cc_start: 0.7797 (m-40) cc_final: 0.7511 (m-40) REVERT: B 59 TYR cc_start: 0.7060 (m-80) cc_final: 0.5958 (m-80) REVERT: B 191 SER cc_start: 0.7925 (t) cc_final: 0.7472 (t) REVERT: B 197 ARG cc_start: 0.7096 (mmt180) cc_final: 0.6568 (mmt180) REVERT: B 214 ARG cc_start: 0.7751 (mpt180) cc_final: 0.6865 (ttp80) REVERT: R 22 ARG cc_start: 0.3856 (mmp-170) cc_final: 0.2745 (mtm-85) REVERT: R 25 PHE cc_start: 0.7066 (t80) cc_final: 0.6264 (t80) REVERT: R 118 MET cc_start: 0.5763 (ttp) cc_final: 0.5381 (mtp) REVERT: R 137 MET cc_start: 0.6656 (tmm) cc_final: 0.6418 (tmm) REVERT: R 196 LEU cc_start: 0.6681 (mt) cc_final: 0.5943 (mt) REVERT: R 290 GLN cc_start: 0.6054 (tp40) cc_final: 0.5634 (tp-100) outliers start: 27 outliers final: 19 residues processed: 173 average time/residue: 0.2196 time to fit residues: 51.8798 Evaluate side-chains 150 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 131 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 302 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 0.0270 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN R 257 GLN R 291 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9218 Z= 0.237 Angle : 0.602 13.590 12502 Z= 0.310 Chirality : 0.043 0.206 1438 Planarity : 0.004 0.063 1589 Dihedral : 5.633 49.644 1279 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.49 % Allowed : 18.38 % Favored : 78.13 % 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: -0.31 (0.25), residues: 1141 helix: 1.02 (0.27), residues: 379 sheet: -0.27 (0.33), residues: 252 loop : -1.07 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 PHE 0.015 0.001 PHE R 27 TYR 0.017 0.001 TYR N 236 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 131 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.6554 (tttp) cc_final: 0.6081 (ttmm) REVERT: A 166 GLU cc_start: 0.6923 (tp30) cc_final: 0.6707 (tp30) REVERT: A 199 ASP cc_start: 0.6256 (m-30) cc_final: 0.5937 (m-30) REVERT: A 244 ASN cc_start: 0.7764 (m-40) cc_final: 0.7468 (m110) REVERT: B 191 SER cc_start: 0.8054 (t) cc_final: 0.7451 (t) REVERT: B 197 ARG cc_start: 0.6933 (mmt180) cc_final: 0.6673 (mmt180) REVERT: B 214 ARG cc_start: 0.7588 (mpt180) cc_final: 0.6941 (ttp80) REVERT: N 74 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.6983 (m-30) REVERT: N 236 TYR cc_start: 0.5238 (OUTLIER) cc_final: 0.4460 (t80) REVERT: G 37 LEU cc_start: 0.4678 (OUTLIER) cc_final: 0.4327 (tt) REVERT: G 38 MET cc_start: 0.6692 (mmm) cc_final: 0.6483 (mmm) REVERT: R 25 PHE cc_start: 0.7137 (t80) cc_final: 0.6315 (t80) REVERT: R 118 MET cc_start: 0.5710 (OUTLIER) cc_final: 0.5294 (mtp) REVERT: R 137 MET cc_start: 0.6384 (tmm) cc_final: 0.6119 (tmm) REVERT: R 215 ASN cc_start: 0.7743 (m-40) cc_final: 0.7090 (m-40) REVERT: R 294 GLN cc_start: 0.6766 (OUTLIER) cc_final: 0.6167 (pp30) outliers start: 34 outliers final: 19 residues processed: 157 average time/residue: 0.2256 time to fit residues: 48.6186 Evaluate side-chains 149 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 194 SER Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 294 GLN Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-dev-5409/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-dev-5409/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: 59.9435 > 50: distance: 112 - 114: 5.811 distance: 114 - 115: 5.001 distance: 115 - 116: 5.164 distance: 116 - 117: 8.492 distance: 116 - 124: 8.358 distance: 118 - 119: 7.583 distance: 119 - 120: 10.675 distance: 119 - 121: 7.774 distance: 120 - 122: 6.646 distance: 121 - 123: 5.847 distance: 122 - 123: 7.206 distance: 124 - 125: 6.145 distance: 125 - 126: 8.157 distance: 125 - 128: 6.311 distance: 126 - 127: 13.691 distance: 126 - 132: 6.588 distance: 128 - 129: 10.289 distance: 129 - 130: 5.535 distance: 129 - 131: 12.855 distance: 132 - 133: 6.313 distance: 133 - 134: 3.112 distance: 134 - 135: 7.791 distance: 134 - 140: 14.235 distance: 136 - 137: 10.020 distance: 137 - 138: 5.968 distance: 137 - 139: 6.151 distance: 140 - 141: 18.378 distance: 141 - 142: 9.746 distance: 141 - 144: 9.637 distance: 142 - 143: 32.051 distance: 142 - 151: 29.053 distance: 144 - 145: 19.497 distance: 145 - 146: 7.715 distance: 147 - 148: 7.982 distance: 148 - 149: 10.387 distance: 148 - 150: 5.116 distance: 151 - 152: 24.396 distance: 152 - 153: 9.598 distance: 152 - 155: 27.415 distance: 153 - 154: 10.991 distance: 153 - 158: 14.813 distance: 155 - 156: 17.293 distance: 155 - 157: 21.605 distance: 158 - 159: 7.234 distance: 159 - 160: 6.287 distance: 159 - 162: 7.032 distance: 160 - 161: 8.431 distance: 160 - 164: 9.774 distance: 162 - 163: 7.170 distance: 164 - 165: 12.907 distance: 164 - 226: 10.740 distance: 165 - 166: 21.001 distance: 165 - 168: 22.847 distance: 166 - 167: 22.391 distance: 166 - 170: 22.168 distance: 167 - 223: 28.699 distance: 168 - 169: 33.510 distance: 170 - 171: 12.986 distance: 171 - 172: 6.204 distance: 171 - 174: 11.684 distance: 172 - 178: 8.765 distance: 174 - 175: 8.664 distance: 175 - 176: 7.459 distance: 175 - 177: 5.206 distance: 178 - 179: 4.696 distance: 178 - 214: 5.311 distance: 179 - 180: 6.410 distance: 180 - 181: 3.332 distance: 181 - 211: 5.118 distance: 182 - 183: 4.982 distance: 183 - 186: 5.114 distance: 186 - 187: 7.754 distance: 186 - 188: 6.930