Starting phenix.real_space_refine on Sat Aug 23 21:57:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m66_30114/08_2025/6m66_30114.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m66_30114/08_2025/6m66_30114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m66_30114/08_2025/6m66_30114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m66_30114/08_2025/6m66_30114.map" model { file = "/net/cci-nas-00/data/ceres_data/6m66_30114/08_2025/6m66_30114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m66_30114/08_2025/6m66_30114.cif" } resolution = 4.1 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= 0.015 sd= 0.098 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 70 5.16 5 C 9975 2.51 5 N 2303 2.21 5 O 2590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s 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: 14938 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 1.79, per 1000 atoms: 0.12 Number of scatterers: 14938 At special positions: 0 Unit cell: (113.94, 113.94, 113.94, 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 70 16.00 O 2590 8.00 N 2303 7.00 C 9975 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.02 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.02 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.02 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.02 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.02 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.02 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.02 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 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 617.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 7 sheets defined 72.5% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 35 through 59 removed outlier: 5.032A pdb=" N ILE A 41 " --> pdb=" O MET A 37 " (cutoff:3.500A) Proline residue: A 46 - end of helix removed outlier: 3.698A pdb=" N GLN A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.595A pdb=" N HIS A 106 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 131 removed outlier: 4.106A pdb=" N LEU A 115 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 157 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 209 through 238 removed outlier: 3.770A pdb=" N TYR A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG A 217 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 220 " --> pdb=" O CYS A 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY A 232 " --> pdb=" O CYS A 228 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 256 removed outlier: 4.139A pdb=" N ASN A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 removed outlier: 4.121A pdb=" N VAL A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 310 removed outlier: 4.442A pdb=" N GLU A 310 " --> pdb=" O LYS A 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 307 through 310' Processing helix chain 'A' and resid 311 through 321 removed outlier: 3.750A pdb=" N ASP A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 336 Processing helix chain 'B' and resid 36 through 59 removed outlier: 5.032A pdb=" N ILE B 41 " --> pdb=" O MET B 37 " (cutoff:3.500A) Proline residue: B 46 - end of helix removed outlier: 3.698A pdb=" N GLN B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 Processing helix chain 'B' and resid 103 through 107 removed outlier: 3.596A pdb=" N HIS B 106 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 131 removed outlier: 4.107A pdb=" N LEU B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 157 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 209 through 238 removed outlier: 3.770A pdb=" N TYR B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG B 217 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 220 " --> pdb=" O CYS B 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY B 232 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR B 234 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 256 removed outlier: 4.139A pdb=" N ASN B 255 " --> pdb=" O GLY B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU B 281 " --> pdb=" O SER B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 removed outlier: 4.121A pdb=" N VAL B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 295 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 310 removed outlier: 4.442A pdb=" N GLU B 310 " --> pdb=" O LYS B 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 307 through 310' Processing helix chain 'B' and resid 311 through 321 removed outlier: 3.750A pdb=" N ASP B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL B 317 " --> pdb=" O PRO B 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'C' and resid 36 through 59 removed outlier: 5.032A pdb=" N ILE C 41 " --> pdb=" O MET C 37 " (cutoff:3.500A) Proline residue: C 46 - end of helix removed outlier: 3.698A pdb=" N GLN C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 87 Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.595A pdb=" N HIS C 106 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 131 removed outlier: 4.107A pdb=" N LEU C 115 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 157 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 209 through 238 removed outlier: 3.770A pdb=" N TYR C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG C 217 " --> pdb=" O TYR C 213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR C 220 " --> pdb=" O CYS C 216 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY C 232 " --> pdb=" O CYS C 228 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR C 234 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE C 235 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER C 236 " --> pdb=" O GLY C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 256 removed outlier: 4.139A pdb=" N ASN C 255 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU C 275 " --> pdb=" O GLY C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU C 281 " --> pdb=" O SER C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 295 removed outlier: 4.121A pdb=" N VAL C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 295 " --> pdb=" O VAL C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 310 removed outlier: 4.442A pdb=" N GLU C 310 " --> pdb=" O LYS C 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 307 through 310' Processing helix chain 'C' and resid 311 through 321 removed outlier: 3.749A pdb=" N ASP C 316 " --> pdb=" O LEU C 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL C 317 " --> pdb=" O PRO C 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 336 Processing helix chain 'D' and resid 36 through 59 removed outlier: 5.032A pdb=" N ILE D 41 " --> pdb=" O MET D 37 " (cutoff:3.500A) Proline residue: D 46 - end of helix removed outlier: 3.698A pdb=" N GLN D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 87 Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.596A pdb=" N HIS D 106 " --> pdb=" O LEU D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 131 removed outlier: 4.107A pdb=" N LEU D 115 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU D 120 " --> pdb=" O PHE D 116 " (cutoff:3.500A) Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 157 Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 198 through 203 Processing helix chain 'D' and resid 209 through 238 removed outlier: 3.770A pdb=" N TYR D 213 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG D 217 " --> pdb=" O TYR D 213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR D 220 " --> pdb=" O CYS D 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY D 232 " --> pdb=" O CYS D 228 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR D 234 " --> pdb=" O TYR D 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE D 235 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER D 236 " --> pdb=" O GLY D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 256 removed outlier: 4.139A pdb=" N ASN D 255 " --> pdb=" O GLY D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU D 275 " --> pdb=" O GLY D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 295 removed outlier: 4.121A pdb=" N VAL D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR D 294 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU D 295 " --> pdb=" O VAL D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 310 removed outlier: 4.443A pdb=" N GLU D 310 " --> pdb=" O LYS D 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 307 through 310' Processing helix chain 'D' and resid 311 through 321 removed outlier: 3.749A pdb=" N ASP D 316 " --> pdb=" O LEU D 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL D 317 " --> pdb=" O PRO D 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 336 Processing helix chain 'E' and resid 36 through 59 removed outlier: 5.031A pdb=" N ILE E 41 " --> pdb=" O MET E 37 " (cutoff:3.500A) Proline residue: E 46 - end of helix removed outlier: 3.697A pdb=" N GLN E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 87 Processing helix chain 'E' and resid 103 through 107 removed outlier: 3.596A pdb=" N HIS E 106 " --> pdb=" O LEU E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 131 removed outlier: 4.107A pdb=" N LEU E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 157 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 198 through 203 Processing helix chain 'E' and resid 209 through 238 removed outlier: 3.770A pdb=" N TYR E 213 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS E 216 " --> pdb=" O LYS E 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG E 217 " --> pdb=" O TYR E 213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR E 220 " --> pdb=" O CYS E 216 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE E 223 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY E 232 " --> pdb=" O CYS E 228 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR E 234 " --> pdb=" O TYR E 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE E 235 " --> pdb=" O LEU E 231 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER E 236 " --> pdb=" O GLY E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 256 removed outlier: 4.139A pdb=" N ASN E 255 " --> pdb=" O GLY E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU E 275 " --> pdb=" O GLY E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU E 281 " --> pdb=" O SER E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 295 removed outlier: 4.121A pdb=" N VAL E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR E 294 " --> pdb=" O VAL E 290 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU E 295 " --> pdb=" O VAL E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 310 removed outlier: 4.442A pdb=" N GLU E 310 " --> pdb=" O LYS E 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 307 through 310' Processing helix chain 'E' and resid 311 through 321 removed outlier: 3.750A pdb=" N ASP E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL E 317 " --> pdb=" O PRO E 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS E 319 " --> pdb=" O PHE E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 336 Processing helix chain 'F' and resid 36 through 59 removed outlier: 5.032A pdb=" N ILE F 41 " --> pdb=" O MET F 37 " (cutoff:3.500A) Proline residue: F 46 - end of helix removed outlier: 3.697A pdb=" N GLN F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 87 Processing helix chain 'F' and resid 103 through 107 removed outlier: 3.596A pdb=" N HIS F 106 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 131 removed outlier: 4.107A pdb=" N LEU F 115 " --> pdb=" O TYR F 111 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 157 Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 198 through 203 Processing helix chain 'F' and resid 209 through 238 removed outlier: 3.771A pdb=" N TYR F 213 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS F 216 " --> pdb=" O LYS F 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG F 217 " --> pdb=" O TYR F 213 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR F 220 " --> pdb=" O CYS F 216 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE F 223 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY F 232 " --> pdb=" O CYS F 228 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR F 234 " --> pdb=" O TYR F 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE F 235 " --> pdb=" O LEU F 231 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 256 removed outlier: 4.139A pdb=" N ASN F 255 " --> pdb=" O GLY F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU F 275 " --> pdb=" O GLY F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU F 281 " --> pdb=" O SER F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 295 removed outlier: 4.121A pdb=" N VAL F 292 " --> pdb=" O ALA F 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR F 294 " --> pdb=" O VAL F 290 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU F 295 " --> pdb=" O VAL F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 310 removed outlier: 4.442A pdb=" N GLU F 310 " --> pdb=" O LYS F 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 307 through 310' Processing helix chain 'F' and resid 311 through 321 removed outlier: 3.750A pdb=" N ASP F 316 " --> pdb=" O LEU F 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL F 317 " --> pdb=" O PRO F 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS F 319 " --> pdb=" O PHE F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 336 Processing helix chain 'G' and resid 36 through 59 removed outlier: 5.032A pdb=" N ILE G 41 " --> pdb=" O MET G 37 " (cutoff:3.500A) Proline residue: G 46 - end of helix removed outlier: 3.697A pdb=" N GLN G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 87 Processing helix chain 'G' and resid 103 through 107 removed outlier: 3.596A pdb=" N HIS G 106 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 131 removed outlier: 4.106A pdb=" N LEU G 115 " --> pdb=" O TYR G 111 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU G 120 " --> pdb=" O PHE G 116 " (cutoff:3.500A) Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 157 Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 198 through 203 Processing helix chain 'G' and resid 209 through 238 removed outlier: 3.770A pdb=" N TYR G 213 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS G 216 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG G 217 " --> pdb=" O TYR G 213 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR G 220 " --> pdb=" O CYS G 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE G 223 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY G 232 " --> pdb=" O CYS G 228 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR G 234 " --> pdb=" O TYR G 230 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE G 235 " --> pdb=" O LEU G 231 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER G 236 " --> pdb=" O GLY G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 256 removed outlier: 4.138A pdb=" N ASN G 255 " --> pdb=" O GLY G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU G 275 " --> pdb=" O GLY G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU G 281 " --> pdb=" O SER G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 295 removed outlier: 4.120A pdb=" N VAL G 292 " --> pdb=" O ALA G 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR G 294 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU G 295 " --> pdb=" O VAL G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 310 removed outlier: 4.442A pdb=" N GLU G 310 " --> pdb=" O LYS G 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 307 through 310' Processing helix chain 'G' and resid 311 through 321 removed outlier: 3.750A pdb=" N ASP G 316 " --> pdb=" O LEU G 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL G 317 " --> pdb=" O PRO G 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS G 319 " --> pdb=" O PHE G 315 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 336 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 3.911A pdb=" N LYS A 266 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 65 removed outlier: 3.911A pdb=" N LYS B 266 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 65 removed outlier: 3.910A pdb=" N LYS C 266 " --> pdb=" O SER C 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 65 removed outlier: 3.911A pdb=" N LYS D 266 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 65 removed outlier: 3.910A pdb=" N LYS E 266 " --> pdb=" O SER E 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 65 removed outlier: 3.911A pdb=" N LYS F 266 " --> pdb=" O SER F 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 65 removed outlier: 3.911A pdb=" N LYS G 266 " --> pdb=" O SER G 65 " (cutoff:3.500A) 736 hydrogen bonds defined for protein. 2187 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: 1.91 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4322 1.34 - 1.46: 3089 1.46 - 1.57: 7814 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 15309 Sorted by residual: bond pdb=" C VAL C 297 " pdb=" N PRO C 298 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.28e-02 6.10e+03 3.95e+00 bond pdb=" C VAL A 297 " pdb=" N PRO A 298 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.28e-02 6.10e+03 3.83e+00 bond pdb=" C VAL G 297 " pdb=" N PRO G 298 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.28e-02 6.10e+03 3.82e+00 bond pdb=" C VAL E 297 " pdb=" N PRO E 298 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.28e-02 6.10e+03 3.80e+00 bond pdb=" C VAL D 297 " pdb=" N PRO D 298 " ideal model delta sigma weight residual 1.335 1.359 -0.025 1.28e-02 6.10e+03 3.75e+00 ... (remaining 15304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 19352 1.74 - 3.47: 1098 3.47 - 5.21: 222 5.21 - 6.95: 91 6.95 - 8.68: 62 Bond angle restraints: 20825 Sorted by residual: angle pdb=" N LEU B 122 " pdb=" CA LEU B 122 " pdb=" C LEU B 122 " ideal model delta sigma weight residual 109.81 117.99 -8.18 2.21e+00 2.05e-01 1.37e+01 angle pdb=" N LEU G 122 " pdb=" CA LEU G 122 " pdb=" C LEU G 122 " ideal model delta sigma weight residual 109.81 117.98 -8.17 2.21e+00 2.05e-01 1.37e+01 angle pdb=" N LEU D 122 " pdb=" CA LEU D 122 " pdb=" C LEU D 122 " ideal model delta sigma weight residual 109.81 117.97 -8.16 2.21e+00 2.05e-01 1.36e+01 angle pdb=" N LEU F 122 " pdb=" CA LEU F 122 " pdb=" C LEU F 122 " ideal model delta sigma weight residual 109.81 117.96 -8.15 2.21e+00 2.05e-01 1.36e+01 angle pdb=" N LEU A 122 " pdb=" CA LEU A 122 " pdb=" C LEU A 122 " ideal model delta sigma weight residual 109.81 117.95 -8.14 2.21e+00 2.05e-01 1.36e+01 ... (remaining 20820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.27: 7305 14.27 - 28.53: 1291 28.53 - 42.80: 420 42.80 - 57.07: 84 57.07 - 71.33: 14 Dihedral angle restraints: 9114 sinusoidal: 3563 harmonic: 5551 Sorted by residual: dihedral pdb=" CA PRO C 260 " pdb=" C PRO C 260 " pdb=" N ASP C 261 " pdb=" CA ASP C 261 " ideal model delta harmonic sigma weight residual -180.00 -155.96 -24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA PRO A 260 " pdb=" C PRO A 260 " pdb=" N ASP A 261 " pdb=" CA ASP A 261 " ideal model delta harmonic sigma weight residual 180.00 -155.97 -24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA PRO D 260 " pdb=" C PRO D 260 " pdb=" N ASP D 261 " pdb=" CA ASP D 261 " ideal model delta harmonic sigma weight residual -180.00 -155.98 -24.02 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 9111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1431 0.045 - 0.091: 758 0.091 - 0.136: 183 0.136 - 0.181: 85 0.181 - 0.226: 14 Chirality restraints: 2471 Sorted by residual: chirality pdb=" CA PHE C 109 " pdb=" N PHE C 109 " pdb=" C PHE C 109 " pdb=" CB PHE C 109 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA PHE A 109 " pdb=" N PHE A 109 " pdb=" C PHE A 109 " pdb=" CB PHE A 109 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA PHE F 109 " pdb=" N PHE F 109 " pdb=" C PHE F 109 " pdb=" CB PHE F 109 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 2468 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 123 " -0.054 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO A 124 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO G 123 " 0.054 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO G 124 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO G 124 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 124 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 123 " -0.054 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO C 124 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO C 124 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 124 " -0.045 5.00e-02 4.00e+02 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2999 2.76 - 3.30: 14723 3.30 - 3.83: 25889 3.83 - 4.37: 28545 4.37 - 4.90: 46095 Nonbonded interactions: 118251 Sorted by model distance: nonbonded pdb=" OH TYR C 111 " pdb=" O LEU D 275 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR D 111 " pdb=" O LEU E 275 " model vdw 2.257 3.040 nonbonded pdb=" O ARG G 217 " pdb=" OG1 THR G 220 " model vdw 2.279 3.040 nonbonded pdb=" O ARG C 217 " pdb=" OG1 THR C 220 " model vdw 2.280 3.040 nonbonded pdb=" O ARG F 217 " pdb=" OG1 THR F 220 " model vdw 2.280 3.040 ... (remaining 118246 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.520 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 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 : 0.005 0.054 15323 Z= 0.263 Angle : 1.076 8.681 20853 Z= 0.566 Chirality : 0.060 0.226 2471 Planarity : 0.010 0.080 2520 Dihedral : 16.352 71.333 5460 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.00 % Allowed : 14.94 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.00 (0.14), residues: 1827 helix: -3.08 (0.11), residues: 1008 sheet: -4.52 (0.40), residues: 70 loop : -3.38 (0.19), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 254 TYR 0.017 0.002 TYR F 309 PHE 0.028 0.002 PHE E 109 TRP 0.008 0.002 TRP E 127 HIS 0.004 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00544 (15309) covalent geometry : angle 1.07623 (20825) SS BOND : bond 0.00522 ( 14) SS BOND : angle 1.14911 ( 28) hydrogen bonds : bond 0.22734 ( 736) hydrogen bonds : angle 8.24486 ( 2187) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 VAL cc_start: 0.9217 (t) cc_final: 0.8970 (p) REVERT: A 144 GLU cc_start: 0.9404 (tm-30) cc_final: 0.9186 (tm-30) REVERT: B 38 VAL cc_start: 0.9216 (t) cc_final: 0.8999 (p) REVERT: B 128 ARG cc_start: 0.9427 (tmm-80) cc_final: 0.9216 (ttp-110) REVERT: B 141 PHE cc_start: 0.7595 (m-10) cc_final: 0.7358 (m-80) REVERT: B 144 GLU cc_start: 0.9464 (tm-30) cc_final: 0.9194 (tm-30) REVERT: C 141 PHE cc_start: 0.7613 (m-10) cc_final: 0.7411 (m-80) REVERT: C 144 GLU cc_start: 0.9422 (tm-30) cc_final: 0.9219 (tm-30) REVERT: C 152 ARG cc_start: 0.5779 (ttt180) cc_final: 0.5517 (ptt90) REVERT: D 128 ARG cc_start: 0.9498 (tmm-80) cc_final: 0.9250 (ttp-110) REVERT: D 141 PHE cc_start: 0.7765 (m-10) cc_final: 0.7422 (m-80) REVERT: D 144 GLU cc_start: 0.9451 (tm-30) cc_final: 0.9154 (tm-30) REVERT: D 152 ARG cc_start: 0.5509 (ttt180) cc_final: 0.5176 (ptt90) REVERT: E 128 ARG cc_start: 0.9452 (tmm-80) cc_final: 0.9141 (ttp-110) REVERT: F 38 VAL cc_start: 0.9311 (t) cc_final: 0.9097 (p) REVERT: F 152 ARG cc_start: 0.5709 (ttt180) cc_final: 0.5467 (ptt90) REVERT: G 38 VAL cc_start: 0.9324 (t) cc_final: 0.9100 (p) REVERT: G 144 GLU cc_start: 0.9419 (tm-30) cc_final: 0.9180 (tm-30) REVERT: G 152 ARG cc_start: 0.5803 (ttt180) cc_final: 0.5523 (ptt90) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.1200 time to fit residues: 42.1158 Evaluate side-chains 130 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 319 HIS A 332 ASN B 134 HIS B 319 HIS C 134 HIS C 319 HIS C 332 ASN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS D 319 HIS E 134 HIS E 319 HIS F 134 HIS F 319 HIS G 134 HIS G 319 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.095241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.074176 restraints weight = 67940.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.075830 restraints weight = 43271.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.077029 restraints weight = 32043.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.077733 restraints weight = 26230.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.078089 restraints weight = 23187.660| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 15323 Z= 0.176 Angle : 0.852 9.151 20853 Z= 0.417 Chirality : 0.050 0.218 2471 Planarity : 0.007 0.053 2520 Dihedral : 6.576 22.427 1981 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.52 (0.17), residues: 1827 helix: -1.65 (0.13), residues: 1134 sheet: -4.87 (0.36), residues: 84 loop : -3.04 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 128 TYR 0.030 0.002 TYR E 234 PHE 0.020 0.001 PHE E 141 TRP 0.010 0.002 TRP B 127 HIS 0.003 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00366 (15309) covalent geometry : angle 0.85095 (20825) SS BOND : bond 0.00405 ( 14) SS BOND : angle 1.35767 ( 28) hydrogen bonds : bond 0.05242 ( 736) hydrogen bonds : angle 5.63975 ( 2187) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7977 (mm110) cc_final: 0.7687 (mm110) REVERT: A 128 ARG cc_start: 0.9395 (ttp-110) cc_final: 0.9180 (ttp80) REVERT: A 141 PHE cc_start: 0.7741 (m-10) cc_final: 0.7533 (m-80) REVERT: A 272 ILE cc_start: 0.9326 (pt) cc_final: 0.9020 (tt) REVERT: B 56 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7625 (mm110) REVERT: B 128 ARG cc_start: 0.9563 (tmm-80) cc_final: 0.9276 (ttp-110) REVERT: B 272 ILE cc_start: 0.9221 (pt) cc_final: 0.8910 (tt) REVERT: C 36 LYS cc_start: 0.8710 (tmmt) cc_final: 0.8488 (tptt) REVERT: C 141 PHE cc_start: 0.7640 (m-10) cc_final: 0.7439 (m-80) REVERT: C 152 ARG cc_start: 0.5893 (ttt180) cc_final: 0.5579 (ptt90) REVERT: D 128 ARG cc_start: 0.9508 (tmm-80) cc_final: 0.9292 (ttp-110) REVERT: D 141 PHE cc_start: 0.7693 (m-10) cc_final: 0.7415 (m-80) REVERT: D 152 ARG cc_start: 0.5398 (ttt180) cc_final: 0.5111 (ptt90) REVERT: E 56 GLN cc_start: 0.7885 (mm110) cc_final: 0.7542 (mm110) REVERT: E 128 ARG cc_start: 0.9493 (tmm-80) cc_final: 0.9156 (ttp-110) REVERT: E 272 ILE cc_start: 0.9297 (pt) cc_final: 0.9052 (tt) REVERT: F 141 PHE cc_start: 0.7812 (m-10) cc_final: 0.7580 (m-80) REVERT: F 152 ARG cc_start: 0.5664 (ttt180) cc_final: 0.5422 (ptt90) REVERT: G 128 ARG cc_start: 0.9418 (ttp-110) cc_final: 0.9208 (ttp80) REVERT: G 141 PHE cc_start: 0.7672 (m-10) cc_final: 0.7439 (m-80) REVERT: G 152 ARG cc_start: 0.5716 (ttt180) cc_final: 0.5471 (ptt90) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1205 time to fit residues: 31.3221 Evaluate side-chains 109 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 135 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 156 optimal weight: 20.0000 chunk 108 optimal weight: 0.8980 chunk 158 optimal weight: 0.0170 chunk 116 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 overall best weight: 1.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 GLN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 ASN E 207 ASN F 332 ASN ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 332 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.096377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.076219 restraints weight = 66275.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.077369 restraints weight = 43591.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.078168 restraints weight = 32328.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.078452 restraints weight = 28939.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.078529 restraints weight = 26539.659| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15323 Z= 0.142 Angle : 0.785 9.191 20853 Z= 0.380 Chirality : 0.048 0.188 2471 Planarity : 0.007 0.053 2520 Dihedral : 6.025 21.149 1981 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.87 (0.18), residues: 1827 helix: -1.08 (0.14), residues: 1134 sheet: -4.09 (0.48), residues: 84 loop : -3.00 (0.22), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 128 TYR 0.019 0.001 TYR E 234 PHE 0.021 0.001 PHE B 141 TRP 0.011 0.001 TRP G 127 HIS 0.001 0.001 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00300 (15309) covalent geometry : angle 0.78451 (20825) SS BOND : bond 0.00223 ( 14) SS BOND : angle 1.11114 ( 28) hydrogen bonds : bond 0.04522 ( 736) hydrogen bonds : angle 5.10343 ( 2187) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.9425 (ttp-110) cc_final: 0.9193 (ttp-110) REVERT: A 141 PHE cc_start: 0.7698 (m-10) cc_final: 0.7411 (m-80) REVERT: B 128 ARG cc_start: 0.9607 (tmm-80) cc_final: 0.9322 (ttp-110) REVERT: C 36 LYS cc_start: 0.8928 (tmmt) cc_final: 0.8678 (tptt) REVERT: C 56 GLN cc_start: 0.8081 (mm110) cc_final: 0.7200 (mm-40) REVERT: D 141 PHE cc_start: 0.7704 (m-10) cc_final: 0.7406 (m-80) REVERT: D 152 ARG cc_start: 0.5367 (ttt180) cc_final: 0.5068 (ptt90) REVERT: E 56 GLN cc_start: 0.8049 (mm110) cc_final: 0.7679 (mm110) REVERT: E 128 ARG cc_start: 0.9576 (tmm-80) cc_final: 0.9237 (ttp-110) REVERT: F 56 GLN cc_start: 0.8112 (mt0) cc_final: 0.7829 (mm110) REVERT: F 141 PHE cc_start: 0.7770 (m-10) cc_final: 0.7557 (m-80) REVERT: F 272 ILE cc_start: 0.9315 (pt) cc_final: 0.8998 (tt) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1064 time to fit residues: 25.7840 Evaluate side-chains 115 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 51.1668 > 50: distance: 27 - 54: 25.011 distance: 31 - 36: 14.140 distance: 32 - 60: 7.984 distance: 36 - 37: 6.155 distance: 37 - 38: 7.846 distance: 37 - 40: 15.432 distance: 38 - 39: 9.245 distance: 38 - 46: 4.190 distance: 39 - 66: 11.633 distance: 40 - 41: 9.613 distance: 41 - 42: 27.951 distance: 41 - 43: 21.053 distance: 42 - 44: 16.696 distance: 43 - 45: 14.776 distance: 44 - 45: 15.681 distance: 46 - 47: 9.493 distance: 47 - 48: 21.610 distance: 47 - 50: 16.437 distance: 48 - 49: 17.730 distance: 48 - 54: 27.564 distance: 49 - 74: 35.040 distance: 50 - 51: 4.971 distance: 50 - 52: 19.806 distance: 51 - 53: 24.960 distance: 54 - 55: 23.989 distance: 55 - 56: 11.276 distance: 55 - 58: 23.325 distance: 56 - 57: 8.870 distance: 56 - 60: 12.173 distance: 57 - 82: 14.169 distance: 58 - 59: 15.938 distance: 60 - 61: 11.210 distance: 61 - 62: 3.245 distance: 62 - 63: 14.458 distance: 62 - 66: 8.731 distance: 63 - 91: 10.940 distance: 64 - 65: 21.174 distance: 66 - 67: 19.098 distance: 67 - 68: 6.528 distance: 67 - 70: 3.860 distance: 68 - 69: 6.284 distance: 68 - 74: 13.931 distance: 69 - 102: 18.916 distance: 70 - 71: 11.563 distance: 71 - 72: 22.004 distance: 71 - 73: 23.325 distance: 74 - 75: 13.998 distance: 75 - 76: 5.380 distance: 75 - 78: 11.942 distance: 76 - 77: 20.780 distance: 76 - 82: 3.111 distance: 77 - 110: 20.093 distance: 78 - 79: 15.664 distance: 79 - 80: 7.397 distance: 79 - 81: 14.383 distance: 82 - 83: 12.577 distance: 83 - 84: 13.573 distance: 83 - 86: 19.046 distance: 84 - 85: 6.951 distance: 84 - 91: 19.484 distance: 85 - 118: 19.395 distance: 86 - 87: 34.370 distance: 87 - 88: 8.941 distance: 88 - 89: 13.790 distance: 89 - 90: 22.103 distance: 91 - 92: 10.988 distance: 92 - 93: 7.146 distance: 92 - 95: 10.702 distance: 93 - 94: 10.497 distance: 93 - 102: 11.686 distance: 94 - 126: 4.827 distance: 95 - 96: 13.720 distance: 96 - 97: 9.723 distance: 96 - 98: 12.652 distance: 97 - 99: 11.142 distance: 98 - 100: 5.798 distance: 99 - 101: 6.855 distance: 100 - 101: 9.607 distance: 102 - 103: 3.364 distance: 103 - 104: 7.385 distance: 103 - 106: 5.797 distance: 104 - 105: 4.709 distance: 104 - 110: 7.838 distance: 105 - 135: 7.419 distance: 106 - 107: 7.983 distance: 106 - 108: 20.496 distance: 107 - 109: 19.212 distance: 110 - 111: 6.179 distance: 111 - 112: 4.197 distance: 111 - 114: 10.257 distance: 112 - 113: 5.633 distance: 112 - 118: 5.567 distance: 113 - 143: 8.055 distance: 114 - 115: 11.037 distance: 115 - 116: 17.179 distance: 116 - 117: 18.663