Starting phenix.real_space_refine on Fri Aug 22 22:50:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xav_33100/08_2025/7xav_33100.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xav_33100/08_2025/7xav_33100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xav_33100/08_2025/7xav_33100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xav_33100/08_2025/7xav_33100.map" model { file = "/net/cci-nas-00/data/ceres_data/7xav_33100/08_2025/7xav_33100.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xav_33100/08_2025/7xav_33100.cif" } resolution = 2.87 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 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= 0.004 sd= 0.128 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 5319 2.51 5 N 1436 2.21 5 O 1601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8410 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 1896 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 11, 'TRANS': 268} Chain breaks: 1 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 441 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 11, 'TYR:plan': 1, 'ARG:plan': 6, 'ASP:plan': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'TRP:plan': 5, 'ASN:plan1': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 184 Chain: "B" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1602 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 2, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 6, 'HIS:plan': 1, 'ARG:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 115 Chain: "C" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "D" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Classifications: {'peptide': 4} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 3} Time building chain proxies: 2.11, per 1000 atoms: 0.25 Number of scatterers: 8410 At special positions: 0 Unit cell: (87.74, 121.98, 127.33, 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 1601 8.00 N 1436 7.00 C 5319 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 149 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.05 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 7 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 TRANS " DTR F 4 " - " TYR F 3 " Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 448.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTR F 4 " Number of C-beta restraints generated: 2132 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 14 sheets defined 30.2% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 43 through 61 removed outlier: 4.025A pdb=" N THR A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 55 " --> pdb=" O PHE A 51 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE A 56 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 77 through 92 removed outlier: 3.654A pdb=" N TYR A 81 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 83 " --> pdb=" O ASN A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 101 removed outlier: 3.819A pdb=" N MET A 101 " --> pdb=" O PRO A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 113 through 125 removed outlier: 4.776A pdb=" N MET A 119 " --> pdb=" O CYS A 115 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N THR A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 123 " --> pdb=" O MET A 119 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 145 removed outlier: 3.518A pdb=" N TYR A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 170 removed outlier: 3.622A pdb=" N SER A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 180 removed outlier: 3.657A pdb=" N ILE A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 219 through 236 removed outlier: 4.626A pdb=" N ILE A 231 " --> pdb=" O CYS A 227 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A 234 " --> pdb=" O PHE A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 249 removed outlier: 4.061A pdb=" N LYS A 249 " --> pdb=" O LYS A 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 246 through 249' Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 259 through 281 removed outlier: 3.626A pdb=" N PHE A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) Proline residue: A 271 - end of helix removed outlier: 3.639A pdb=" N SER A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 294 through 299 removed outlier: 3.703A pdb=" N VAL A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 312 Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 316 through 326 Processing helix chain 'B' and resid 8 through 26 removed outlier: 3.758A pdb=" N MET B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN B 22 " --> pdb=" O MET B 18 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU B 25 " --> pdb=" O ARG B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.641A pdb=" N LYS B 51 " --> pdb=" O ASN B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 4.595A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS B 214 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.533A pdb=" N TYR B 230 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 255 removed outlier: 3.626A pdb=" N ASN B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 279 removed outlier: 3.644A pdb=" N PHE B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 301 Processing helix chain 'B' and resid 302 through 309 Processing helix chain 'B' and resid 332 through 351 removed outlier: 3.514A pdb=" N ASP B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 25 removed outlier: 3.642A pdb=" N GLU C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS C 15 " --> pdb=" O ALA C 11 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN C 17 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.814A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 22 removed outlier: 3.804A pdb=" N ALA D 12 " --> pdb=" O SER D 8 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU D 15 " --> pdb=" O GLN D 11 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 16 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 34 through 42 removed outlier: 3.694A pdb=" N CYS D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 184 Processing sheet with id=AA2, first strand: chain 'B' and resid 185 through 188 removed outlier: 6.194A pdb=" N VAL B 34 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE B 199 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU B 36 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N ALA B 220 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LEU B 39 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 52 removed outlier: 6.048A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS C 337 " --> pdb=" O THR C 329 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.594A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 3.964A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.887A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 7.041A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.264A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 275 through 277 removed outlier: 3.504A pdb=" N CYS C 294 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.561A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.654A pdb=" N TYR E 59 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.933A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR E 243 " --> pdb=" O TYR E 227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 155 through 160 removed outlier: 3.751A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 189 through 190 289 hydrogen bonds defined for protein. 795 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: 1.20 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2544 1.33 - 1.46: 2293 1.46 - 1.59: 3655 1.59 - 1.72: 0 1.72 - 1.85: 75 Bond restraints: 8567 Sorted by residual: bond pdb=" CB VAL C 112 " pdb=" CG2 VAL C 112 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 7.02e+00 bond pdb=" CG1 ILE C 338 " pdb=" CD1 ILE C 338 " ideal model delta sigma weight residual 1.513 1.415 0.098 3.90e-02 6.57e+02 6.35e+00 bond pdb=" CG1 ILE C 58 " pdb=" CD1 ILE C 58 " ideal model delta sigma weight residual 1.513 1.422 0.091 3.90e-02 6.57e+02 5.46e+00 bond pdb=" CA SER B 16 " pdb=" CB SER B 16 " ideal model delta sigma weight residual 1.529 1.490 0.039 1.74e-02 3.30e+03 5.10e+00 bond pdb=" CB CYS C 317 " pdb=" SG CYS C 317 " ideal model delta sigma weight residual 1.808 1.737 0.071 3.30e-02 9.18e+02 4.65e+00 ... (remaining 8562 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 11490 3.53 - 7.07: 150 7.07 - 10.60: 19 10.60 - 14.14: 0 14.14 - 17.67: 1 Bond angle restraints: 11660 Sorted by residual: angle pdb=" C THR B 190 " pdb=" N PHE B 191 " pdb=" CA PHE B 191 " ideal model delta sigma weight residual 122.58 114.37 8.21 2.07e+00 2.33e-01 1.57e+01 angle pdb=" C ASP C 246 " pdb=" N ASP C 247 " pdb=" CA ASP C 247 " ideal model delta sigma weight residual 121.52 130.50 -8.98 2.34e+00 1.83e-01 1.47e+01 angle pdb=" C ASP C 291 " pdb=" N PHE C 292 " pdb=" CA PHE C 292 " ideal model delta sigma weight residual 125.66 132.54 -6.88 1.85e+00 2.92e-01 1.38e+01 angle pdb=" C ASN C 88 " pdb=" CA ASN C 88 " pdb=" CB ASN C 88 " ideal model delta sigma weight residual 109.38 115.72 -6.34 1.80e+00 3.09e-01 1.24e+01 angle pdb=" C ASP C 333 " pdb=" N SER C 334 " pdb=" CA SER C 334 " ideal model delta sigma weight residual 121.54 128.02 -6.48 1.91e+00 2.74e-01 1.15e+01 ... (remaining 11655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.39: 4441 15.39 - 30.77: 480 30.77 - 46.15: 118 46.15 - 61.54: 24 61.54 - 76.92: 7 Dihedral angle restraints: 5070 sinusoidal: 1769 harmonic: 3301 Sorted by residual: dihedral pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual 93.00 161.80 -68.80 1 1.00e+01 1.00e-02 6.13e+01 dihedral pdb=" CB CYS F 2 " pdb=" SG CYS F 2 " pdb=" SG CYS F 7 " pdb=" CB CYS F 7 " ideal model delta sinusoidal sigma weight residual -86.00 -31.70 -54.30 1 1.00e+01 1.00e-02 4.00e+01 dihedral pdb=" CB CYS A 115 " pdb=" SG CYS A 115 " pdb=" SG CYS A 193 " pdb=" CB CYS A 193 " ideal model delta sinusoidal sigma weight residual -86.00 -33.81 -52.19 1 1.00e+01 1.00e-02 3.72e+01 ... (remaining 5067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 911 0.054 - 0.108: 342 0.108 - 0.162: 90 0.162 - 0.216: 24 0.216 - 0.270: 9 Chirality restraints: 1376 Sorted by residual: chirality pdb=" CB VAL B 218 " pdb=" CA VAL B 218 " pdb=" CG1 VAL B 218 " pdb=" CG2 VAL B 218 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA CYS F 2 " pdb=" N CYS F 2 " pdb=" C CYS F 2 " pdb=" CB CYS F 2 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB VAL A 145 " pdb=" CA VAL A 145 " pdb=" CG1 VAL A 145 " pdb=" CG2 VAL A 145 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1373 not shown) Planarity restraints: 1490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 175 " -0.052 5.00e-02 4.00e+02 7.86e-02 9.87e+00 pdb=" N PRO A 176 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 319 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.29e+00 pdb=" C ILE B 319 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE B 319 " -0.019 2.00e-02 2.50e+03 pdb=" N TYR B 320 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 151 " -0.029 2.00e-02 2.50e+03 1.99e-02 6.92e+00 pdb=" CG PHE C 151 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE C 151 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE C 151 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 151 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE C 151 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 151 " -0.007 2.00e-02 2.50e+03 ... (remaining 1487 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.18: 1 2.18 - 2.86: 3112 2.86 - 3.54: 10857 3.54 - 4.22: 20826 4.22 - 4.90: 35098 Nonbonded interactions: 69894 Sorted by model distance: nonbonded pdb=" CG2 THR A 212 " pdb=" CZ3 DTR F 4 " model vdw 1.494 3.760 nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.181 3.040 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.240 3.040 nonbonded pdb=" O ASP E 223 " pdb=" OH TYR E 227 " model vdw 2.240 3.040 nonbonded pdb=" OG1 THR C 274 " pdb=" O GLY C 288 " model vdw 2.252 3.040 ... (remaining 69889 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.540 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 : 0.009 0.098 8573 Z= 0.398 Angle : 1.053 17.673 11673 Z= 0.568 Chirality : 0.064 0.270 1376 Planarity : 0.007 0.079 1489 Dihedral : 14.144 76.924 2920 Min Nonbonded Distance : 1.494 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 0.71 % Allowed : 10.12 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.66 (0.20), residues: 1120 helix: -4.55 (0.13), residues: 343 sheet: -1.92 (0.30), residues: 257 loop : -2.53 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 21 TYR 0.035 0.003 TYR C 105 PHE 0.042 0.004 PHE C 151 TRP 0.023 0.003 TRP C 99 HIS 0.008 0.002 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00915 ( 8567) covalent geometry : angle 1.05126 (11660) SS BOND : bond 0.01405 ( 5) SS BOND : angle 2.55916 ( 10) hydrogen bonds : bond 0.29973 ( 289) hydrogen bonds : angle 11.03237 ( 795) link_TRANS : bond 0.00501 ( 1) link_TRANS : angle 0.28799 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 183 time to evaluate : 0.340 Fit side-chains REVERT: A 122 ASP cc_start: 0.6663 (m-30) cc_final: 0.6404 (m-30) REVERT: A 173 VAL cc_start: 0.8208 (t) cc_final: 0.7973 (p) REVERT: A 180 TYR cc_start: 0.7658 (m-80) cc_final: 0.7038 (m-80) REVERT: A 196 ASN cc_start: 0.7340 (m110) cc_final: 0.7107 (m110) REVERT: B 24 ARG cc_start: 0.7468 (ttp-110) cc_final: 0.7040 (ttp-110) REVERT: B 262 THR cc_start: 0.8514 (p) cc_final: 0.8314 (p) REVERT: B 333 GLN cc_start: 0.8052 (tp40) cc_final: 0.7446 (tp40) REVERT: C 154 ASP cc_start: 0.7530 (m-30) cc_final: 0.7283 (m-30) REVERT: C 175 GLN cc_start: 0.7974 (pt0) cc_final: 0.7554 (pp30) REVERT: C 215 GLU cc_start: 0.7278 (tp30) cc_final: 0.6770 (tp30) REVERT: E 19 LYS cc_start: 0.8430 (tttp) cc_final: 0.8096 (tppp) REVERT: E 38 ARG cc_start: 0.8021 (ptt180) cc_final: 0.7785 (ptp-170) outliers start: 6 outliers final: 2 residues processed: 187 average time/residue: 0.5289 time to fit residues: 105.4657 Evaluate side-chains 154 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN B 188 HIS B 346 ASN B 347 ASN C 62 HIS C 239 ASN E 39 GLN E 113 GLN E 142 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.204422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.147275 restraints weight = 9979.200| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.18 r_work: 0.3524 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8573 Z= 0.174 Angle : 0.677 12.200 11673 Z= 0.355 Chirality : 0.045 0.239 1376 Planarity : 0.005 0.058 1489 Dihedral : 6.280 37.586 1219 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.53 % Allowed : 16.59 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.75 (0.22), residues: 1120 helix: -3.38 (0.19), residues: 364 sheet: -1.72 (0.29), residues: 280 loop : -2.01 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 160 TYR 0.018 0.002 TYR C 59 PHE 0.017 0.002 PHE C 151 TRP 0.015 0.002 TRP C 99 HIS 0.005 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 8567) covalent geometry : angle 0.67588 (11660) SS BOND : bond 0.00820 ( 5) SS BOND : angle 1.62364 ( 10) hydrogen bonds : bond 0.04603 ( 289) hydrogen bonds : angle 6.30027 ( 795) link_TRANS : bond 0.00434 ( 1) link_TRANS : angle 0.36989 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 176 time to evaluate : 0.337 Fit side-chains REVERT: A 93 MET cc_start: 0.6962 (mmm) cc_final: 0.6703 (tpt) REVERT: A 122 ASP cc_start: 0.6952 (m-30) cc_final: 0.6371 (t0) REVERT: A 196 ASN cc_start: 0.7311 (m110) cc_final: 0.6976 (m110) REVERT: A 209 ILE cc_start: 0.7557 (pt) cc_final: 0.7340 (mp) REVERT: A 302 TYR cc_start: 0.8150 (m-80) cc_final: 0.7850 (m-80) REVERT: B 24 ARG cc_start: 0.7768 (ttp-110) cc_final: 0.7130 (ttp-110) REVERT: B 262 THR cc_start: 0.8561 (p) cc_final: 0.8262 (t) REVERT: B 333 GLN cc_start: 0.7850 (tp40) cc_final: 0.7282 (tp40) REVERT: C 154 ASP cc_start: 0.7961 (m-30) cc_final: 0.7676 (m-30) REVERT: C 175 GLN cc_start: 0.8410 (pt0) cc_final: 0.7716 (pp30) REVERT: C 197 ARG cc_start: 0.7796 (mmm160) cc_final: 0.7578 (mmm-85) REVERT: C 284 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7087 (tp) REVERT: E 19 LYS cc_start: 0.8478 (tttp) cc_final: 0.8001 (tppp) REVERT: E 234 GLU cc_start: 0.8466 (pt0) cc_final: 0.8074 (pt0) outliers start: 30 outliers final: 11 residues processed: 193 average time/residue: 0.5046 time to fit residues: 104.1623 Evaluate side-chains 168 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 19 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 46 optimal weight: 0.0980 chunk 102 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.204702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.147881 restraints weight = 9811.467| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.14 r_work: 0.3532 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8573 Z= 0.162 Angle : 0.636 12.434 11673 Z= 0.332 Chirality : 0.045 0.161 1376 Planarity : 0.005 0.057 1489 Dihedral : 5.868 42.757 1219 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 5.06 % Allowed : 19.06 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.07 (0.23), residues: 1120 helix: -2.50 (0.23), residues: 362 sheet: -1.45 (0.29), residues: 276 loop : -1.83 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 160 TYR 0.016 0.002 TYR E 103 PHE 0.017 0.002 PHE C 151 TRP 0.013 0.002 TRP C 99 HIS 0.004 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 8567) covalent geometry : angle 0.63360 (11660) SS BOND : bond 0.01127 ( 5) SS BOND : angle 2.15722 ( 10) hydrogen bonds : bond 0.03779 ( 289) hydrogen bonds : angle 5.60786 ( 795) link_TRANS : bond 0.00234 ( 1) link_TRANS : angle 0.20010 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 158 time to evaluate : 0.297 Fit side-chains REVERT: A 180 TYR cc_start: 0.7319 (m-80) cc_final: 0.6751 (m-10) REVERT: A 196 ASN cc_start: 0.7344 (m110) cc_final: 0.7121 (m110) REVERT: A 302 TYR cc_start: 0.8146 (m-80) cc_final: 0.7919 (m-80) REVERT: B 9 ASP cc_start: 0.8349 (m-30) cc_final: 0.7883 (m-30) REVERT: B 24 ARG cc_start: 0.7888 (ttp-110) cc_final: 0.7276 (ttp-110) REVERT: B 262 THR cc_start: 0.8626 (p) cc_final: 0.8321 (t) REVERT: B 333 GLN cc_start: 0.7867 (tp40) cc_final: 0.7377 (tp40) REVERT: C 154 ASP cc_start: 0.7959 (m-30) cc_final: 0.7625 (m-30) REVERT: C 175 GLN cc_start: 0.8397 (pt0) cc_final: 0.7721 (pp30) REVERT: C 275 SER cc_start: 0.8308 (OUTLIER) cc_final: 0.8055 (m) REVERT: C 284 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6978 (tp) REVERT: C 325 MET cc_start: 0.8007 (tpp) cc_final: 0.7590 (mmt) REVERT: E 19 LYS cc_start: 0.8484 (tttp) cc_final: 0.7920 (tppp) REVERT: E 76 LYS cc_start: 0.8076 (mptt) cc_final: 0.7855 (mttp) REVERT: E 234 GLU cc_start: 0.8480 (pt0) cc_final: 0.8146 (pt0) outliers start: 43 outliers final: 18 residues processed: 187 average time/residue: 0.5039 time to fit residues: 100.8073 Evaluate side-chains 166 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 215 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 50.0000 chunk 71 optimal weight: 0.0870 chunk 99 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 239 ASN C 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.203215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.146053 restraints weight = 10076.635| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.49 r_work: 0.3487 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8573 Z= 0.194 Angle : 0.668 12.082 11673 Z= 0.347 Chirality : 0.046 0.186 1376 Planarity : 0.004 0.057 1489 Dihedral : 5.811 49.827 1219 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 5.76 % Allowed : 20.24 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.74 (0.24), residues: 1120 helix: -2.01 (0.25), residues: 356 sheet: -1.50 (0.28), residues: 286 loop : -1.67 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 160 TYR 0.018 0.002 TYR E 103 PHE 0.022 0.002 PHE C 151 TRP 0.015 0.002 TRP C 99 HIS 0.005 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 8567) covalent geometry : angle 0.66460 (11660) SS BOND : bond 0.01293 ( 5) SS BOND : angle 2.32009 ( 10) hydrogen bonds : bond 0.03711 ( 289) hydrogen bonds : angle 5.44599 ( 795) link_TRANS : bond 0.00256 ( 1) link_TRANS : angle 0.18475 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 146 time to evaluate : 0.213 Fit side-chains REVERT: A 180 TYR cc_start: 0.7359 (m-80) cc_final: 0.6681 (m-10) REVERT: B 9 ASP cc_start: 0.8271 (m-30) cc_final: 0.7740 (m-30) REVERT: B 24 ARG cc_start: 0.7597 (ttp-110) cc_final: 0.6984 (ttp-110) REVERT: B 191 PHE cc_start: 0.7006 (OUTLIER) cc_final: 0.5479 (p90) REVERT: B 262 THR cc_start: 0.8659 (p) cc_final: 0.8348 (t) REVERT: C 154 ASP cc_start: 0.7775 (m-30) cc_final: 0.7448 (m-30) REVERT: C 175 GLN cc_start: 0.8327 (pt0) cc_final: 0.7589 (pp30) REVERT: C 217 MET cc_start: 0.6746 (ppp) cc_final: 0.6544 (pp-130) REVERT: C 275 SER cc_start: 0.8290 (OUTLIER) cc_final: 0.7961 (m) REVERT: C 325 MET cc_start: 0.7769 (tpp) cc_final: 0.7348 (mmt) REVERT: E 19 LYS cc_start: 0.8464 (tttp) cc_final: 0.7882 (tppp) REVERT: E 76 LYS cc_start: 0.8158 (mptt) cc_final: 0.7954 (mttp) REVERT: E 83 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.7005 (ptt) REVERT: E 234 GLU cc_start: 0.8328 (pt0) cc_final: 0.7938 (pt0) outliers start: 49 outliers final: 30 residues processed: 178 average time/residue: 0.4590 time to fit residues: 87.5008 Evaluate side-chains 174 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 215 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 4.9990 chunk 104 optimal weight: 0.0570 chunk 76 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 107 optimal weight: 0.0060 chunk 58 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 46 optimal weight: 0.0870 chunk 27 optimal weight: 7.9990 overall best weight: 0.4092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN C 259 GLN E 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.208973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.152936 restraints weight = 10005.616| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.18 r_work: 0.3593 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8573 Z= 0.104 Angle : 0.579 12.763 11673 Z= 0.297 Chirality : 0.042 0.143 1376 Planarity : 0.004 0.053 1489 Dihedral : 5.282 54.956 1219 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.00 % Allowed : 23.06 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (0.24), residues: 1120 helix: -1.69 (0.25), residues: 373 sheet: -1.24 (0.30), residues: 273 loop : -1.66 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 160 TYR 0.012 0.001 TYR A 211 PHE 0.028 0.001 PHE B 189 TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 8567) covalent geometry : angle 0.57835 (11660) SS BOND : bond 0.00693 ( 5) SS BOND : angle 1.35989 ( 10) hydrogen bonds : bond 0.02868 ( 289) hydrogen bonds : angle 4.92770 ( 795) link_TRANS : bond 0.00014 ( 1) link_TRANS : angle 0.47852 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.324 Fit side-chains REVERT: A 63 LEU cc_start: 0.7448 (mm) cc_final: 0.7212 (mt) REVERT: A 173 VAL cc_start: 0.7965 (t) cc_final: 0.7738 (p) REVERT: A 180 TYR cc_start: 0.7201 (m-80) cc_final: 0.6585 (m-10) REVERT: A 218 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7069 (tp) REVERT: B 21 ARG cc_start: 0.8169 (ptp90) cc_final: 0.7772 (mtm110) REVERT: B 24 ARG cc_start: 0.7848 (ttp-110) cc_final: 0.7285 (ttp-110) REVERT: B 262 THR cc_start: 0.8464 (p) cc_final: 0.8228 (t) REVERT: B 274 PHE cc_start: 0.5950 (OUTLIER) cc_final: 0.5462 (p90) REVERT: C 175 GLN cc_start: 0.8126 (pt0) cc_final: 0.7525 (pp30) REVERT: C 275 SER cc_start: 0.8254 (OUTLIER) cc_final: 0.8022 (m) REVERT: C 290 ASP cc_start: 0.6542 (OUTLIER) cc_final: 0.6294 (p0) REVERT: C 325 MET cc_start: 0.7969 (tpp) cc_final: 0.7588 (mmt) REVERT: E 19 LYS cc_start: 0.8458 (tttp) cc_final: 0.7975 (tppp) outliers start: 34 outliers final: 17 residues processed: 181 average time/residue: 0.5032 time to fit residues: 97.1794 Evaluate side-chains 166 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 155 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 80 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 99 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 46 optimal weight: 0.0980 chunk 16 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 68 optimal weight: 0.0980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 ASN C 237 ASN E 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.209149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.154187 restraints weight = 9963.386| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.51 r_work: 0.3590 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8573 Z= 0.102 Angle : 0.568 12.230 11673 Z= 0.291 Chirality : 0.042 0.176 1376 Planarity : 0.004 0.049 1489 Dihedral : 5.103 58.239 1219 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.47 % Allowed : 23.06 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.25), residues: 1120 helix: -1.27 (0.26), residues: 369 sheet: -0.90 (0.31), residues: 267 loop : -1.59 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 304 TYR 0.016 0.001 TYR E 173 PHE 0.022 0.001 PHE C 241 TRP 0.012 0.001 TRP C 82 HIS 0.002 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 8567) covalent geometry : angle 0.56694 (11660) SS BOND : bond 0.00665 ( 5) SS BOND : angle 1.26501 ( 10) hydrogen bonds : bond 0.02755 ( 289) hydrogen bonds : angle 4.74196 ( 795) link_TRANS : bond 0.00043 ( 1) link_TRANS : angle 0.47906 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.348 Fit side-chains REVERT: A 63 LEU cc_start: 0.7467 (mm) cc_final: 0.7227 (mt) REVERT: A 180 TYR cc_start: 0.7098 (m-80) cc_final: 0.6487 (m-10) REVERT: A 218 LEU cc_start: 0.7270 (mm) cc_final: 0.6947 (tp) REVERT: B 24 ARG cc_start: 0.7717 (ttp-110) cc_final: 0.7204 (ttp-110) REVERT: B 308 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: C 175 GLN cc_start: 0.8033 (pt0) cc_final: 0.7517 (pp30) REVERT: C 275 SER cc_start: 0.8079 (OUTLIER) cc_final: 0.7853 (m) REVERT: C 325 MET cc_start: 0.7831 (tpp) cc_final: 0.7490 (mmt) REVERT: E 19 LYS cc_start: 0.8426 (tttp) cc_final: 0.7948 (tppp) REVERT: E 186 GLN cc_start: 0.7687 (tm-30) cc_final: 0.7481 (tm-30) REVERT: E 189 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7764 (mp) REVERT: E 214 LEU cc_start: 0.5806 (OUTLIER) cc_final: 0.4900 (tp) outliers start: 38 outliers final: 19 residues processed: 182 average time/residue: 0.5415 time to fit residues: 105.2159 Evaluate side-chains 167 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 214 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 ASN C 295 ASN E 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.207808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.151078 restraints weight = 9999.154| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.20 r_work: 0.3585 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8573 Z= 0.127 Angle : 0.593 11.849 11673 Z= 0.306 Chirality : 0.043 0.165 1376 Planarity : 0.004 0.050 1489 Dihedral : 5.185 59.786 1219 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.59 % Allowed : 24.47 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.25), residues: 1120 helix: -1.00 (0.27), residues: 362 sheet: -0.85 (0.31), residues: 269 loop : -1.43 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 304 TYR 0.024 0.002 TYR A 205 PHE 0.029 0.002 PHE C 241 TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8567) covalent geometry : angle 0.59165 (11660) SS BOND : bond 0.00919 ( 5) SS BOND : angle 1.63961 ( 10) hydrogen bonds : bond 0.02875 ( 289) hydrogen bonds : angle 4.81759 ( 795) link_TRANS : bond 0.00089 ( 1) link_TRANS : angle 0.50970 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 0.372 Fit side-chains REVERT: A 61 ASN cc_start: 0.7475 (m-40) cc_final: 0.7203 (m-40) REVERT: A 180 TYR cc_start: 0.7158 (m-80) cc_final: 0.6523 (m-10) REVERT: A 218 LEU cc_start: 0.7321 (mm) cc_final: 0.7008 (tp) REVERT: B 21 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7812 (mtm110) REVERT: B 24 ARG cc_start: 0.7887 (ttp-110) cc_final: 0.7307 (ttp-110) REVERT: C 175 GLN cc_start: 0.8160 (pt0) cc_final: 0.7571 (pp30) REVERT: C 234 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8543 (m-80) REVERT: C 275 SER cc_start: 0.8197 (OUTLIER) cc_final: 0.7903 (m) REVERT: C 325 MET cc_start: 0.8002 (tpp) cc_final: 0.7620 (mmt) REVERT: D 47 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6559 (pm20) REVERT: E 19 LYS cc_start: 0.8398 (tttp) cc_final: 0.8006 (tppp) REVERT: E 160 ARG cc_start: 0.6187 (mmm160) cc_final: 0.5936 (mmm160) REVERT: E 186 GLN cc_start: 0.7906 (tm-30) cc_final: 0.7678 (tm-30) REVERT: E 189 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7883 (mp) REVERT: E 214 LEU cc_start: 0.5905 (OUTLIER) cc_final: 0.4959 (tp) outliers start: 39 outliers final: 21 residues processed: 182 average time/residue: 0.5234 time to fit residues: 101.8973 Evaluate side-chains 175 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 214 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 41 optimal weight: 0.6980 chunk 14 optimal weight: 40.0000 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 0.0770 chunk 84 optimal weight: 9.9990 chunk 13 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.209701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.153997 restraints weight = 9929.290| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.54 r_work: 0.3600 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8573 Z= 0.111 Angle : 0.587 11.894 11673 Z= 0.302 Chirality : 0.043 0.146 1376 Planarity : 0.004 0.048 1489 Dihedral : 5.031 54.322 1219 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.88 % Allowed : 25.06 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.25), residues: 1120 helix: -0.81 (0.28), residues: 360 sheet: -0.84 (0.31), residues: 272 loop : -1.30 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 304 TYR 0.010 0.001 TYR E 173 PHE 0.025 0.001 PHE C 241 TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 8567) covalent geometry : angle 0.58541 (11660) SS BOND : bond 0.00644 ( 5) SS BOND : angle 1.37243 ( 10) hydrogen bonds : bond 0.02704 ( 289) hydrogen bonds : angle 4.74945 ( 795) link_TRANS : bond 0.00124 ( 1) link_TRANS : angle 0.65867 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 61 ASN cc_start: 0.7347 (m-40) cc_final: 0.7121 (m-40) REVERT: A 173 VAL cc_start: 0.8103 (t) cc_final: 0.7888 (p) REVERT: A 180 TYR cc_start: 0.7175 (m-80) cc_final: 0.6482 (m-10) REVERT: A 205 TYR cc_start: 0.5854 (t80) cc_final: 0.5647 (OUTLIER) REVERT: B 21 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7603 (mtt90) REVERT: B 24 ARG cc_start: 0.7687 (ttp-110) cc_final: 0.7122 (ttp-110) REVERT: C 175 GLN cc_start: 0.8054 (pt0) cc_final: 0.7580 (pp30) REVERT: C 234 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8507 (m-80) REVERT: C 275 SER cc_start: 0.7987 (OUTLIER) cc_final: 0.7656 (m) REVERT: C 325 MET cc_start: 0.7818 (tpp) cc_final: 0.7502 (mmt) REVERT: D 47 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6427 (pm20) REVERT: E 19 LYS cc_start: 0.8333 (tttp) cc_final: 0.7966 (tppp) REVERT: E 76 LYS cc_start: 0.8259 (mptt) cc_final: 0.7798 (ptpt) REVERT: E 189 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7833 (mp) REVERT: E 214 LEU cc_start: 0.5758 (OUTLIER) cc_final: 0.4879 (tp) REVERT: E 220 GLU cc_start: 0.7458 (mp0) cc_final: 0.6929 (mp0) outliers start: 33 outliers final: 20 residues processed: 167 average time/residue: 0.4993 time to fit residues: 88.9747 Evaluate side-chains 164 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 214 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.2258 > 50: distance: 114 - 159: 28.997 distance: 117 - 156: 35.360 distance: 137 - 143: 34.887 distance: 143 - 144: 44.217 distance: 144 - 145: 25.117 distance: 144 - 147: 22.340 distance: 145 - 146: 8.912 distance: 149 - 150: 20.760 distance: 149 - 155: 3.597 distance: 150 - 151: 25.154 distance: 151 - 152: 13.924 distance: 151 - 156: 15.216 distance: 153 - 154: 33.193 distance: 154 - 155: 9.919 distance: 156 - 157: 27.648 distance: 157 - 158: 30.327 distance: 157 - 160: 11.359 distance: 158 - 159: 8.828 distance: 158 - 165: 27.563 distance: 165 - 166: 5.685 distance: 166 - 167: 27.236 distance: 166 - 169: 4.472 distance: 167 - 168: 31.550 distance: 167 - 173: 23.134 distance: 169 - 170: 8.587 distance: 170 - 171: 58.120 distance: 170 - 172: 20.872 distance: 173 - 174: 38.314 distance: 174 - 175: 29.906 distance: 175 - 176: 9.663 distance: 175 - 181: 30.897 distance: 177 - 178: 40.760 distance: 181 - 182: 28.959 distance: 182 - 183: 6.493 distance: 182 - 185: 11.515 distance: 183 - 184: 8.877 distance: 183 - 189: 15.944 distance: 185 - 186: 25.090 distance: 185 - 187: 56.973 distance: 186 - 188: 14.338 distance: 189 - 190: 7.393 distance: 189 - 229: 23.369 distance: 190 - 191: 6.055 distance: 190 - 193: 10.804 distance: 191 - 192: 43.322 distance: 191 - 201: 18.627 distance: 192 - 226: 37.096 distance: 193 - 194: 41.948 distance: 194 - 195: 37.449 distance: 194 - 196: 22.817 distance: 195 - 197: 40.491 distance: 197 - 199: 18.240 distance: 198 - 199: 22.647 distance: 199 - 200: 7.208 distance: 201 - 202: 41.624 distance: 202 - 203: 13.345 distance: 202 - 205: 19.590 distance: 203 - 212: 22.030 distance: 205 - 206: 34.388 distance: 207 - 208: 20.930 distance: 208 - 209: 60.242 distance: 209 - 211: 6.668 distance: 212 - 213: 17.157 distance: 213 - 214: 40.004 distance: 213 - 216: 41.057 distance: 214 - 215: 39.117 distance: 216 - 217: 7.821 distance: 217 - 218: 8.718 distance: 218 - 219: 56.934 distance: 220 - 221: 25.575 distance: 221 - 222: 26.184 distance: 221 - 224: 19.987 distance: 222 - 223: 11.293 distance: 222 - 226: 28.250 distance: 224 - 225: 22.467