Starting phenix.real_space_refine on Thu Jan 18 01:13:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvw_32860/01_2024/7wvw_32860_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvw_32860/01_2024/7wvw_32860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvw_32860/01_2024/7wvw_32860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvw_32860/01_2024/7wvw_32860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvw_32860/01_2024/7wvw_32860_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvw_32860/01_2024/7wvw_32860_updated.pdb" } resolution = 3.1 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= 0.004 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 54 5.16 5 C 4608 2.51 5 N 1212 2.21 5 O 1295 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 310": "OD1" <-> "OD2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 42": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 7169 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 65 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2344 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 285} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1753 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2583 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 424 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 4.26, per 1000 atoms: 0.59 Number of scatterers: 7169 At special positions: 0 Unit cell: (114.95, 119.13, 84.645, 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 54 16.00 O 1295 8.00 N 1212 7.00 C 4608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " 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: 2.80 Conformation dependent library (CDL) restraints added in 1.3 seconds 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1734 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 9 sheets defined 43.7% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'R' and resid 20 through 54 Proline residue: R 29 - end of helix removed outlier: 3.737A pdb=" N PHE R 53 " --> pdb=" O TRP R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 86 Proline residue: R 79 - end of helix Processing helix chain 'R' and resid 95 through 128 Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 139 through 162 removed outlier: 4.089A pdb=" N GLY R 148 " --> pdb=" O LYS R 144 " (cutoff:3.500A) Proline residue: R 149 - end of helix Proline residue: R 159 - end of helix Processing helix chain 'R' and resid 187 through 208 Processing helix chain 'R' and resid 211 through 230 Processing helix chain 'R' and resid 238 through 266 Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 268 through 273 Processing helix chain 'R' and resid 279 through 302 removed outlier: 4.388A pdb=" N ASN R 285 " --> pdb=" O ASP R 281 " (cutoff:3.500A) Proline residue: R 286 - end of helix Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 307 through 316 Processing helix chain 'A' and resid 7 through 31 removed outlier: 3.798A pdb=" N GLU A 25 " --> pdb=" O LYS A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 removed outlier: 3.888A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.726A pdb=" N TYR A 231 " --> pdb=" O LEU A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 272 through 281 removed outlier: 4.051A pdb=" N GLU A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N HIS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 297 through 311 Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.653A pdb=" N LEU C 15 " --> pdb=" O GLN C 11 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.783A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'R' and resid 164 through 168 removed outlier: 3.501A pdb=" N THR R 177 " --> pdb=" O THR R 165 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 320 through 324 removed outlier: 6.455A pdb=" N ILE A 265 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N HIS A 323 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU A 267 " --> pdb=" O HIS A 323 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 37 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 39 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS A 225 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.032A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 111 through 114 removed outlier: 3.625A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.813A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.687A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.734A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.411A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 46 through 52 removed outlier: 3.604A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 1020 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: 2.16 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2294 1.35 - 1.47: 1778 1.47 - 1.59: 3168 1.59 - 1.71: 0 1.71 - 1.83: 79 Bond restraints: 7319 Sorted by residual: bond pdb=" SD FME L 1 " pdb=" CE FME L 1 " ideal model delta sigma weight residual 1.805 1.752 0.053 2.00e-02 2.50e+03 6.95e+00 bond pdb=" CG FME L 1 " pdb=" SD FME L 1 " ideal model delta sigma weight residual 1.817 1.770 0.047 2.00e-02 2.50e+03 5.50e+00 bond pdb=" N FME L 1 " pdb=" CN FME L 1 " ideal model delta sigma weight residual 1.335 1.376 -0.041 2.00e-02 2.50e+03 4.24e+00 bond pdb=" N FME L 1 " pdb=" CA FME L 1 " ideal model delta sigma weight residual 1.458 1.437 0.021 1.90e-02 2.77e+03 1.26e+00 bond pdb=" CN FME L 1 " pdb=" O1 FME L 1 " ideal model delta sigma weight residual 1.221 1.241 -0.020 2.00e-02 2.50e+03 9.75e-01 ... (remaining 7314 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.88: 162 106.88 - 113.66: 4097 113.66 - 120.43: 2770 120.43 - 127.21: 2821 127.21 - 133.99: 78 Bond angle restraints: 9928 Sorted by residual: angle pdb=" C TYR R 175 " pdb=" N CYS R 176 " pdb=" CA CYS R 176 " ideal model delta sigma weight residual 122.84 118.55 4.29 1.30e+00 5.92e-01 1.09e+01 angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.71 111.03 2.68 9.50e-01 1.11e+00 7.95e+00 angle pdb=" CA CYS R 176 " pdb=" CB CYS R 176 " pdb=" SG CYS R 176 " ideal model delta sigma weight residual 114.40 120.09 -5.69 2.30e+00 1.89e-01 6.12e+00 angle pdb=" CA LEU R 162 " pdb=" CB LEU R 162 " pdb=" CG LEU R 162 " ideal model delta sigma weight residual 116.30 124.57 -8.27 3.50e+00 8.16e-02 5.58e+00 angle pdb=" C ASP A 329 " pdb=" N THR A 330 " pdb=" CA THR A 330 " ideal model delta sigma weight residual 122.08 125.17 -3.09 1.47e+00 4.63e-01 4.41e+00 ... (remaining 9923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.27: 3850 16.27 - 32.54: 361 32.54 - 48.81: 88 48.81 - 65.08: 9 65.08 - 81.35: 7 Dihedral angle restraints: 4315 sinusoidal: 1641 harmonic: 2674 Sorted by residual: dihedral pdb=" CA PHE R 161 " pdb=" C PHE R 161 " pdb=" N LEU R 162 " pdb=" CA LEU R 162 " ideal model delta harmonic sigma weight residual -180.00 -162.92 -17.08 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ASN A 348 " pdb=" CB ASN A 348 " pdb=" CG ASN A 348 " pdb=" OD1 ASN A 348 " ideal model delta sinusoidal sigma weight residual 120.00 -177.28 -62.72 2 2.00e+01 2.50e-03 9.48e+00 dihedral pdb=" CB MET R 214 " pdb=" CG MET R 214 " pdb=" SD MET R 214 " pdb=" CE MET R 214 " ideal model delta sinusoidal sigma weight residual -180.00 -122.29 -57.71 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 4312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 686 0.027 - 0.053: 280 0.053 - 0.080: 110 0.080 - 0.107: 55 0.107 - 0.133: 28 Chirality restraints: 1159 Sorted by residual: chirality pdb=" CA LEU R 162 " pdb=" N LEU R 162 " pdb=" C LEU R 162 " pdb=" CB LEU R 162 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA VAL C 54 " pdb=" N VAL C 54 " pdb=" C VAL C 54 " pdb=" CB VAL C 54 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 1156 not shown) Planarity restraints: 1243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 148 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.14e+00 pdb=" N PRO R 149 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO R 149 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 149 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.023 5.00e-02 4.00e+02 3.53e-02 2.00e+00 pdb=" N PRO B 236 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 95 " -0.012 2.00e-02 2.50e+03 8.74e-03 1.91e+00 pdb=" CG TRP R 95 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP R 95 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP R 95 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 95 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 95 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 95 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 95 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 95 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP R 95 " -0.001 2.00e-02 2.50e+03 ... (remaining 1240 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 452 2.74 - 3.28: 7268 3.28 - 3.82: 12491 3.82 - 4.36: 14589 4.36 - 4.90: 25401 Nonbonded interactions: 60201 Sorted by model distance: nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.197 2.440 nonbonded pdb=" OD1 ASN A 270 " pdb=" OG1 THR A 325 " model vdw 2.221 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.239 2.440 nonbonded pdb=" OH TYR A 231 " pdb=" OG SER A 282 " model vdw 2.290 2.440 nonbonded pdb=" NH2 ARG B 256 " pdb=" OD2 ASP C 36 " model vdw 2.309 2.520 ... (remaining 60196 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 4.020 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 23.210 Find NCS groups from input model: 0.260 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 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 : 0.002 0.053 7319 Z= 0.137 Angle : 0.496 8.271 9928 Z= 0.266 Chirality : 0.040 0.133 1159 Planarity : 0.003 0.051 1243 Dihedral : 13.512 81.345 2578 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: 0.78 (0.28), residues: 911 helix: 1.80 (0.26), residues: 413 sheet: 0.56 (0.45), residues: 152 loop : -1.09 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 95 HIS 0.004 0.000 HIS R 102 PHE 0.016 0.001 PHE R 161 TYR 0.009 0.001 TYR R 175 ARG 0.013 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.779 Fit side-chains REVERT: R 106 ASP cc_start: 0.7299 (t70) cc_final: 0.7097 (t70) REVERT: R 204 ILE cc_start: 0.7547 (mt) cc_final: 0.6928 (mt) REVERT: A 325 THR cc_start: 0.7395 (m) cc_final: 0.7172 (m) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1907 time to fit residues: 43.2621 Evaluate side-chains 125 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 294 ASN ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 311 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 7319 Z= 0.397 Angle : 0.614 8.165 9928 Z= 0.320 Chirality : 0.046 0.205 1159 Planarity : 0.004 0.047 1243 Dihedral : 4.284 54.476 984 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.69 % Allowed : 12.50 % Favored : 85.81 % 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: 0.74 (0.28), residues: 911 helix: 1.68 (0.25), residues: 421 sheet: 0.26 (0.39), residues: 182 loop : -1.02 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 211 HIS 0.005 0.001 HIS B 62 PHE 0.015 0.002 PHE B 199 TYR 0.012 0.002 TYR C 40 ARG 0.004 0.001 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 0.827 Fit side-chains REVERT: R 87 MET cc_start: 0.6633 (OUTLIER) cc_final: 0.6104 (ptp) REVERT: R 103 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8213 (mp) outliers start: 13 outliers final: 10 residues processed: 155 average time/residue: 0.1814 time to fit residues: 38.4192 Evaluate side-chains 143 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 103 ILE Chi-restraints excluded: chain R residue 171 ASN Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 173 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 27 optimal weight: 0.0370 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 102 HIS ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7319 Z= 0.191 Angle : 0.500 7.920 9928 Z= 0.256 Chirality : 0.041 0.143 1159 Planarity : 0.004 0.049 1243 Dihedral : 4.075 53.903 984 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.82 % Allowed : 14.71 % Favored : 83.46 % 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: 0.82 (0.28), residues: 911 helix: 1.79 (0.25), residues: 423 sheet: 0.22 (0.40), residues: 175 loop : -0.96 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.005 0.001 HIS R 102 PHE 0.017 0.001 PHE B 199 TYR 0.011 0.001 TYR B 111 ARG 0.003 0.000 ARG R 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 1.026 Fit side-chains REVERT: R 103 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8241 (mp) REVERT: A 242 ASN cc_start: 0.7467 (t0) cc_final: 0.6470 (t0) outliers start: 14 outliers final: 9 residues processed: 146 average time/residue: 0.1731 time to fit residues: 34.7121 Evaluate side-chains 140 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 ILE Chi-restraints excluded: chain R residue 171 ASN Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 294 ASN Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 74 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 54 optimal weight: 0.0870 chunk 82 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7319 Z= 0.215 Angle : 0.500 7.933 9928 Z= 0.257 Chirality : 0.042 0.141 1159 Planarity : 0.004 0.048 1243 Dihedral : 4.117 54.694 984 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.08 % Allowed : 15.76 % Favored : 82.16 % 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: 0.83 (0.28), residues: 911 helix: 1.87 (0.26), residues: 423 sheet: -0.04 (0.38), residues: 181 loop : -0.92 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.002 0.001 HIS A 189 PHE 0.016 0.001 PHE B 199 TYR 0.010 0.001 TYR R 175 ARG 0.002 0.000 ARG R 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 0.812 Fit side-chains REVERT: R 27 ILE cc_start: 0.7278 (mm) cc_final: 0.6966 (mt) REVERT: R 103 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8242 (mt) REVERT: A 25 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6673 (mp0) outliers start: 16 outliers final: 13 residues processed: 146 average time/residue: 0.1676 time to fit residues: 34.0691 Evaluate side-chains 136 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 ILE Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 171 ASN Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 294 ASN Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7319 Z= 0.220 Angle : 0.505 7.449 9928 Z= 0.259 Chirality : 0.041 0.136 1159 Planarity : 0.004 0.048 1243 Dihedral : 4.129 55.399 984 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.65 % Allowed : 16.41 % Favored : 79.95 % 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: 0.78 (0.28), residues: 911 helix: 1.88 (0.26), residues: 422 sheet: -0.16 (0.38), residues: 181 loop : -0.95 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.002 0.001 HIS A 189 PHE 0.014 0.001 PHE B 199 TYR 0.010 0.001 TYR R 277 ARG 0.001 0.000 ARG R 238 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 0.841 Fit side-chains REVERT: R 27 ILE cc_start: 0.7251 (mm) cc_final: 0.6894 (mt) REVERT: R 99 LYS cc_start: 0.8073 (tptt) cc_final: 0.7742 (mmtt) REVERT: R 103 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8212 (mt) REVERT: R 143 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7401 (mpp) REVERT: A 25 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6618 (mp0) outliers start: 28 outliers final: 19 residues processed: 148 average time/residue: 0.1738 time to fit residues: 35.6178 Evaluate side-chains 146 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 103 ILE Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 171 ASN Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 294 ASN Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 28 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7319 Z= 0.189 Angle : 0.482 8.245 9928 Z= 0.247 Chirality : 0.041 0.136 1159 Planarity : 0.003 0.048 1243 Dihedral : 4.093 55.322 984 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.65 % Allowed : 17.32 % Favored : 79.04 % 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: 0.80 (0.28), residues: 911 helix: 1.91 (0.26), residues: 421 sheet: -0.24 (0.38), residues: 181 loop : -0.91 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.001 0.000 HIS A 189 PHE 0.014 0.001 PHE B 199 TYR 0.011 0.001 TYR R 277 ARG 0.002 0.000 ARG R 238 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 126 time to evaluate : 0.853 Fit side-chains REVERT: R 27 ILE cc_start: 0.7240 (mm) cc_final: 0.6871 (mt) REVERT: R 87 MET cc_start: 0.6128 (ptm) cc_final: 0.5905 (ptp) REVERT: R 99 LYS cc_start: 0.8076 (tptt) cc_final: 0.7743 (mmtt) REVERT: R 103 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8227 (mt) REVERT: R 143 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7383 (mpp) REVERT: A 25 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6623 (mp0) outliers start: 28 outliers final: 22 residues processed: 145 average time/residue: 0.1697 time to fit residues: 34.0452 Evaluate side-chains 145 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 103 ILE Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 171 ASN Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 294 ASN Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 28 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 48 optimal weight: 0.0000 chunk 86 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7319 Z= 0.191 Angle : 0.502 7.356 9928 Z= 0.258 Chirality : 0.041 0.135 1159 Planarity : 0.004 0.048 1243 Dihedral : 4.059 55.321 984 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.78 % Allowed : 17.84 % Favored : 78.39 % 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: 0.84 (0.28), residues: 911 helix: 1.94 (0.26), residues: 421 sheet: -0.19 (0.37), residues: 186 loop : -0.90 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.001 0.000 HIS R 102 PHE 0.013 0.001 PHE B 199 TYR 0.012 0.001 TYR R 277 ARG 0.002 0.000 ARG R 238 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 0.872 Fit side-chains REVERT: R 27 ILE cc_start: 0.7198 (mm) cc_final: 0.6776 (mt) REVERT: R 87 MET cc_start: 0.6094 (ptm) cc_final: 0.5887 (ptp) REVERT: R 99 LYS cc_start: 0.8088 (tptt) cc_final: 0.7762 (mmtt) REVERT: R 103 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8222 (mt) REVERT: R 143 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.6980 (mpp) REVERT: A 25 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6634 (mp0) outliers start: 29 outliers final: 22 residues processed: 146 average time/residue: 0.1917 time to fit residues: 38.0885 Evaluate side-chains 148 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 123 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 103 ILE Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 171 ASN Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 294 ASN Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 55 optimal weight: 0.4980 chunk 59 optimal weight: 0.0980 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7319 Z= 0.257 Angle : 0.526 7.103 9928 Z= 0.272 Chirality : 0.042 0.150 1159 Planarity : 0.004 0.048 1243 Dihedral : 4.202 56.457 984 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.52 % Allowed : 18.49 % Favored : 77.99 % 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: 0.69 (0.28), residues: 911 helix: 1.89 (0.26), residues: 421 sheet: -0.37 (0.38), residues: 179 loop : -0.99 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 63 HIS 0.002 0.001 HIS A 214 PHE 0.012 0.001 PHE B 199 TYR 0.009 0.001 TYR R 277 ARG 0.004 0.000 ARG R 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 127 time to evaluate : 0.779 Fit side-chains REVERT: R 99 LYS cc_start: 0.8169 (tptt) cc_final: 0.7951 (mmtt) REVERT: R 103 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8200 (mt) REVERT: R 143 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.6954 (mpp) REVERT: R 272 LEU cc_start: 0.8315 (mt) cc_final: 0.8035 (mp) REVERT: A 25 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6572 (mp0) outliers start: 27 outliers final: 22 residues processed: 143 average time/residue: 0.1646 time to fit residues: 32.8634 Evaluate side-chains 145 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 103 ILE Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 171 ASN Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 321 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- 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: 67.6009 > 50: distance: 62 - 146: 22.401 distance: 65 - 143: 12.149 distance: 71 - 79: 23.777 distance: 79 - 80: 10.084 distance: 80 - 81: 17.557 distance: 80 - 83: 8.952 distance: 81 - 82: 16.694 distance: 81 - 87: 18.640 distance: 83 - 84: 12.063 distance: 84 - 85: 8.722 distance: 84 - 86: 9.134 distance: 87 - 88: 20.450 distance: 88 - 89: 9.596 distance: 88 - 91: 5.874 distance: 89 - 90: 16.601 distance: 89 - 94: 15.709 distance: 91 - 92: 17.845 distance: 91 - 93: 26.972 distance: 94 - 95: 22.188 distance: 95 - 96: 29.426 distance: 95 - 98: 18.247 distance: 96 - 97: 7.905 distance: 96 - 105: 48.099 distance: 98 - 99: 7.161 distance: 102 - 103: 3.262 distance: 102 - 104: 23.552 distance: 105 - 106: 33.767 distance: 106 - 107: 27.593 distance: 106 - 109: 26.652 distance: 107 - 108: 8.480 distance: 107 - 114: 31.638 distance: 109 - 110: 11.645 distance: 114 - 115: 7.418 distance: 115 - 116: 3.334 distance: 116 - 117: 18.169 distance: 116 - 118: 47.959 distance: 118 - 119: 17.909 distance: 119 - 120: 9.396 distance: 119 - 122: 26.348 distance: 120 - 121: 5.531 distance: 120 - 126: 26.627 distance: 122 - 123: 29.605 distance: 123 - 124: 20.262 distance: 124 - 125: 42.012 distance: 126 - 127: 16.860 distance: 127 - 130: 7.273 distance: 128 - 129: 5.272 distance: 128 - 132: 5.058 distance: 130 - 131: 23.905 distance: 132 - 133: 15.971 distance: 133 - 134: 11.719 distance: 133 - 136: 22.897 distance: 134 - 135: 9.602 distance: 134 - 143: 6.959 distance: 136 - 137: 12.882 distance: 137 - 138: 4.179 distance: 138 - 139: 3.112 distance: 139 - 140: 5.457 distance: 140 - 141: 9.280 distance: 143 - 144: 12.924 distance: 144 - 145: 8.482 distance: 144 - 147: 12.060 distance: 145 - 146: 10.506 distance: 145 - 152: 5.373 distance: 147 - 148: 20.458 distance: 148 - 149: 20.511 distance: 149 - 150: 17.893 distance: 149 - 151: 10.909 distance: 152 - 153: 19.214 distance: 153 - 156: 15.147 distance: 154 - 155: 14.160 distance: 154 - 159: 9.982 distance: 156 - 157: 8.380 distance: 156 - 158: 12.437