Starting phenix.real_space_refine (version: 1.21rc1) on Wed May 3 12:31:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d85_27247/05_2023/8d85_27247.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d85_27247/05_2023/8d85_27247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d85_27247/05_2023/8d85_27247.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d85_27247/05_2023/8d85_27247.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d85_27247/05_2023/8d85_27247.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d85_27247/05_2023/8d85_27247.pdb" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.019 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 31 5.16 5 C 4527 2.51 5 N 1197 2.21 5 O 1338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 210": "OD1" <-> "OD2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D ASP 89": "OD1" <-> "OD2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D GLU 169": "OE1" <-> "OE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D GLU 174": "OE1" <-> "OE2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 220": "OE1" <-> "OE2" Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 59": "OD1" <-> "OD2" Residue "A GLU 65": "OE1" <-> "OE2" Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "B TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B ARG 176": "NH1" <-> "NH2" Residue "B ASP 177": "OD1" <-> "OD2" Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "B ASP 210": "OD1" <-> "OD2" Residue "B PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 315": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 7093 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1590 Classifications: {'peptide': 201} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 178} Chain: "D" Number of atoms: 1452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1452 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain breaks: 1 Chain: "A" Number of atoms: 1524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1524 Classifications: {'peptide': 191} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 172} Chain: "B" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2373 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 16, 'TRANS': 279} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.46, per 1000 atoms: 0.63 Number of scatterers: 7093 At special positions: 0 Unit cell: (107.5, 104.06, 139.32, 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 31 16.00 O 1338 8.00 N 1197 7.00 C 4527 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 46 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 52 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 54 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 182 " 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A 601 " - " ASN A 76 " " NAG B 701 " - " ASN B 227 " " NAG B 702 " - " ASN B 157 " " NAG B 703 " - " ASN B 131 " " NAG C 301 " - " ASN C 105 " " NAG E 1 " - " ASN A 51 " " NAG F 1 " - " ASN B 83 " " NAG G 1 " - " ASN B 43 " Time building additional restraints: 2.77 Conformation dependent library (CDL) restraints added in 1.2 seconds 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1646 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 18 sheets defined 17.8% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'D' and resid 42 through 73 Processing helix chain 'D' and resid 93 through 100 Processing helix chain 'D' and resid 103 through 124 Proline residue: D 115 - end of helix Processing helix chain 'D' and resid 130 through 158 Processing helix chain 'D' and resid 166 through 179 Processing helix chain 'D' and resid 196 through 225 Processing helix chain 'B' and resid 51 through 58 Processing helix chain 'B' and resid 247 through 251 removed outlier: 4.305A pdb=" N SER B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 removed outlier: 3.643A pdb=" N ALA B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 43 through 46 removed outlier: 4.160A pdb=" N CYS C 46 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS C 89 " --> pdb=" O CYS C 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.649A pdb=" N ILE C 63 " --> pdb=" O THR C 107 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 103 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE C 121 " --> pdb=" O TYR C 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 136 through 138 removed outlier: 3.686A pdb=" N LEU C 145 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 178 through 183 removed outlier: 6.205A pdb=" N TYR C 165 " --> pdb=" O PRO C 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 66 removed outlier: 3.674A pdb=" N GLU A 65 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 108 " --> pdb=" O GLU A 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 102 through 105 removed outlier: 3.526A pdb=" N VAL A 105 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 118 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 132 through 139 removed outlier: 3.829A pdb=" N ARG A 132 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N HIS A 150 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ASP A 136 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N THR A 148 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 177 through 178 removed outlier: 3.869A pdb=" N LEU A 183 " --> pdb=" O CYS A 164 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 177 through 178 Processing sheet with id=AB1, first strand: chain 'A' and resid 202 through 204 removed outlier: 3.561A pdb=" N LEU A 224 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 37 through 38 removed outlier: 3.957A pdb=" N VAL B 38 " --> pdb=" O ILE B 121 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 45 through 47 Processing sheet with id=AB4, first strand: chain 'B' and resid 73 through 74 removed outlier: 4.735A pdb=" N TRP B 67 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 66 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN B 104 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN B 113 " --> pdb=" O ILE B 105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 181 through 183 removed outlier: 4.364A pdb=" N CYS B 182 " --> pdb=" O CYS B 144 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N CYS B 144 " --> pdb=" O CYS B 182 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG B 143 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP B 147 " --> pdb=" O ASN B 131 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASN B 131 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N LYS B 221 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL B 136 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 172 through 173 removed outlier: 3.864A pdb=" N LYS B 161 " --> pdb=" O TRP B 197 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP B 197 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU B 195 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 172 through 173 removed outlier: 3.864A pdb=" N LYS B 161 " --> pdb=" O TRP B 197 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP B 197 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU B 195 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 194 " --> pdb=" O PHE B 214 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE B 214 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL B 196 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE B 212 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 229 through 231 removed outlier: 3.622A pdb=" N THR B 243 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS B 241 " --> pdb=" O ILE B 231 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 270 through 271 removed outlier: 3.987A pdb=" N TYR B 295 " --> pdb=" O GLY B 319 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY B 319 " --> pdb=" O TYR B 295 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 317 " --> pdb=" O PHE B 297 " (cutoff:3.500A) 205 hydrogen bonds defined for protein. 549 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: 2.06 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2263 1.34 - 1.46: 1724 1.46 - 1.58: 3259 1.58 - 1.70: 0 1.70 - 1.82: 43 Bond restraints: 7289 Sorted by residual: bond pdb=" C ASP D 102 " pdb=" N PRO D 103 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.08e-02 8.57e+03 3.24e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" C1 NAG B 702 " pdb=" O5 NAG B 702 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.83e+00 ... (remaining 7284 not shown) Histogram of bond angle deviations from ideal: 100.86 - 107.48: 410 107.48 - 114.11: 4159 114.11 - 120.73: 2687 120.73 - 127.36: 2568 127.36 - 133.98: 117 Bond angle restraints: 9941 Sorted by residual: angle pdb=" CA LEU A 68 " pdb=" CB LEU A 68 " pdb=" CG LEU A 68 " ideal model delta sigma weight residual 116.30 126.43 -10.13 3.50e+00 8.16e-02 8.37e+00 angle pdb=" N SER B 32 " pdb=" CA SER B 32 " pdb=" C SER B 32 " ideal model delta sigma weight residual 109.81 115.62 -5.81 2.21e+00 2.05e-01 6.92e+00 angle pdb=" C VAL C 109 " pdb=" N HIS C 110 " pdb=" CA HIS C 110 " ideal model delta sigma weight residual 121.80 116.20 5.60 2.44e+00 1.68e-01 5.28e+00 angle pdb=" C LEU A 198 " pdb=" N ALA A 199 " pdb=" CA ALA A 199 " ideal model delta sigma weight residual 122.08 125.21 -3.13 1.47e+00 4.63e-01 4.53e+00 angle pdb=" C ILE B 31 " pdb=" N SER B 32 " pdb=" CA SER B 32 " ideal model delta sigma weight residual 121.80 116.99 4.81 2.44e+00 1.68e-01 3.89e+00 ... (remaining 9936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 3951 16.41 - 32.82: 280 32.82 - 49.24: 50 49.24 - 65.65: 5 65.65 - 82.06: 11 Dihedral angle restraints: 4297 sinusoidal: 1764 harmonic: 2533 Sorted by residual: dihedral pdb=" CB CYS C 35 " pdb=" SG CYS C 35 " pdb=" SG CYS C 46 " pdb=" CB CYS C 46 " ideal model delta sinusoidal sigma weight residual -86.00 -43.34 -42.66 1 1.00e+01 1.00e-02 2.54e+01 dihedral pdb=" CA SER B 32 " pdb=" C SER B 32 " pdb=" N PRO B 33 " pdb=" CA PRO B 33 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA TYR B 30 " pdb=" C TYR B 30 " pdb=" N ILE B 31 " pdb=" CA ILE B 31 " ideal model delta harmonic sigma weight residual 180.00 164.46 15.54 0 5.00e+00 4.00e-02 9.65e+00 ... (remaining 4294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 891 0.041 - 0.082: 136 0.082 - 0.122: 92 0.122 - 0.163: 7 0.163 - 0.204: 2 Chirality restraints: 1128 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 51 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C1 NAG C 301 " pdb=" ND2 ASN C 105 " pdb=" C2 NAG C 301 " pdb=" O5 NAG C 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" C1 NAG B 701 " pdb=" ND2 ASN B 227 " pdb=" C2 NAG B 701 " pdb=" O5 NAG B 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.44e-01 ... (remaining 1125 not shown) Planarity restraints: 1264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 102 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO D 103 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 40 " 0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO C 41 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 41 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 41 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 272 " -0.021 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO B 273 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 273 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 273 " -0.018 5.00e-02 4.00e+02 ... (remaining 1261 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 2379 2.87 - 3.37: 6114 3.37 - 3.88: 10679 3.88 - 4.39: 10827 4.39 - 4.90: 19504 Nonbonded interactions: 49503 Sorted by model distance: nonbonded pdb=" NE2 GLN C 81 " pdb=" O SER C 86 " model vdw 2.357 2.520 nonbonded pdb=" NH2 ARG C 168 " pdb=" OE1 GLN C 202 " model vdw 2.367 2.520 nonbonded pdb=" NE1 TRP C 166 " pdb=" OE1 GLN C 206 " model vdw 2.372 2.520 nonbonded pdb=" OE1 GLU B 34 " pdb=" OG SER B 35 " model vdw 2.374 2.440 nonbonded pdb=" ND2 ASN B 246 " pdb=" OG SER B 282 " model vdw 2.381 2.520 ... (remaining 49498 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 'E' selection = chain 'F' selection = chain 'G' } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.260 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: 11.790 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.940 Find NCS groups from input model: 0.270 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: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 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 : 0.003 0.041 7289 Z= 0.167 Angle : 0.531 10.127 9941 Z= 0.261 Chirality : 0.040 0.204 1128 Planarity : 0.003 0.039 1256 Dihedral : 11.745 82.060 2627 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.09 % Favored : 95.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: -2.45 (0.25), residues: 855 helix: 0.17 (0.39), residues: 154 sheet: -0.72 (0.39), residues: 174 loop : -2.67 (0.22), residues: 527 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2527 time to fit residues: 60.5478 Evaluate side-chains 106 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.855 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 HIS ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN D 154 GLN ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN A 159 HIS A 167 HIS B 110 GLN ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN B 211 HIS B 258 ASN B 260 GLN B 271 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 7289 Z= 0.201 Angle : 0.620 9.526 9941 Z= 0.294 Chirality : 0.046 0.537 1128 Planarity : 0.005 0.081 1256 Dihedral : 3.168 27.639 936 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.91 % Favored : 94.97 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: -1.64 (0.27), residues: 855 helix: 1.79 (0.42), residues: 148 sheet: -0.94 (0.34), residues: 205 loop : -2.16 (0.24), residues: 502 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 133 average time/residue: 0.2080 time to fit residues: 36.4134 Evaluate side-chains 109 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 101 time to evaluate : 0.887 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0721 time to fit residues: 2.2248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 150 HIS ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 GLN ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 7289 Z= 0.243 Angle : 0.635 8.851 9941 Z= 0.311 Chirality : 0.046 0.422 1128 Planarity : 0.006 0.092 1256 Dihedral : 3.815 31.134 936 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.20 % Favored : 93.68 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -1.31 (0.28), residues: 855 helix: 2.30 (0.42), residues: 148 sheet: -0.94 (0.32), residues: 228 loop : -1.95 (0.26), residues: 479 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 129 average time/residue: 0.2270 time to fit residues: 38.9397 Evaluate side-chains 100 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.911 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1470 time to fit residues: 3.0165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 73 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 64 GLN D 154 GLN A 71 GLN B 110 GLN B 114 ASN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 7289 Z= 0.279 Angle : 0.708 12.663 9941 Z= 0.338 Chirality : 0.049 0.391 1128 Planarity : 0.006 0.093 1256 Dihedral : 4.448 33.275 936 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.55 % Favored : 93.33 % Rotamer Outliers : 2.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -1.20 (0.28), residues: 855 helix: 2.32 (0.43), residues: 148 sheet: -0.85 (0.30), residues: 239 loop : -1.87 (0.27), residues: 468 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 119 average time/residue: 0.1871 time to fit residues: 30.4273 Evaluate side-chains 96 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.883 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0627 time to fit residues: 2.0443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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: 70.0261 > 50: distance: 4 - 85: 28.985 distance: 7 - 11: 25.183 distance: 11 - 12: 18.551 distance: 12 - 13: 39.698 distance: 12 - 15: 21.676 distance: 13 - 16: 25.574 distance: 16 - 17: 21.674 distance: 17 - 18: 6.549 distance: 18 - 19: 3.302 distance: 18 - 22: 15.871 distance: 22 - 23: 3.378 distance: 23 - 24: 42.059 distance: 23 - 26: 42.503 distance: 24 - 33: 38.484 distance: 26 - 27: 43.590 distance: 27 - 28: 22.769 distance: 30 - 31: 10.664 distance: 34 - 35: 40.701 distance: 35 - 45: 45.881 distance: 38 - 39: 18.145 distance: 39 - 41: 13.927 distance: 40 - 42: 11.699 distance: 41 - 43: 3.226 distance: 42 - 43: 9.528 distance: 45 - 46: 41.423 distance: 45 - 51: 45.322 distance: 46 - 47: 32.774 distance: 46 - 49: 12.509 distance: 47 - 48: 25.194 distance: 49 - 50: 51.758 distance: 50 - 51: 39.511 distance: 53 - 54: 56.229 distance: 53 - 56: 43.242 distance: 54 - 55: 38.929 distance: 54 - 60: 41.210 distance: 56 - 57: 45.096 distance: 56 - 58: 21.425 distance: 61 - 64: 17.818 distance: 62 - 63: 27.810 distance: 65 - 66: 33.070 distance: 65 - 116: 33.171 distance: 66 - 67: 54.159 distance: 66 - 69: 20.699 distance: 67 - 68: 29.841 distance: 68 - 113: 30.358 distance: 69 - 70: 19.862 distance: 69 - 71: 40.797 distance: 73 - 74: 40.084 distance: 74 - 75: 6.347 distance: 74 - 80: 10.560 distance: 77 - 78: 39.119 distance: 80 - 81: 23.679 distance: 81 - 82: 37.407 distance: 82 - 83: 37.166 distance: 82 - 86: 15.756 distance: 84 - 85: 12.397