Starting phenix.real_space_refine on Sun Aug 24 04:52:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fz7_29605/08_2025/8fz7_29605.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fz7_29605/08_2025/8fz7_29605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fz7_29605/08_2025/8fz7_29605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fz7_29605/08_2025/8fz7_29605.map" model { file = "/net/cci-nas-00/data/ceres_data/8fz7_29605/08_2025/8fz7_29605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fz7_29605/08_2025/8fz7_29605.cif" } resolution = 2.88 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= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 P 4 5.49 5 S 68 5.16 5 C 10728 2.51 5 N 2897 2.21 5 O 3272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 16971 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2473 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "B" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' K': 2, 'PGW': 1, 'YQ1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, E, G, D, F, H Time building chain proxies: 3.57, per 1000 atoms: 0.21 Number of scatterers: 16971 At special positions: 0 Unit cell: (150.481, 150.481, 118.003, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 68 16.00 P 4 15.00 O 3272 8.00 N 2897 7.00 C 10728 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.65 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3952 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 16 sheets defined 52.7% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 21 through 43 removed outlier: 3.621A pdb=" N LEU A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 58 removed outlier: 3.502A pdb=" N ALA A 58 " --> pdb=" O PHE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 107 removed outlier: 3.760A pdb=" N MET A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 removed outlier: 3.511A pdb=" N LEU A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.939A pdb=" N ARG A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 151 " --> pdb=" O ASN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.569A pdb=" N LYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 202 removed outlier: 3.545A pdb=" N ILE A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 224 removed outlier: 3.560A pdb=" N ARG A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 242 removed outlier: 3.502A pdb=" N ILE A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 removed outlier: 3.755A pdb=" N MET A 250 " --> pdb=" O GLY A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 323 through 332 removed outlier: 3.694A pdb=" N GLU A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 43 removed outlier: 3.621A pdb=" N LEU C 25 " --> pdb=" O THR C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 58 removed outlier: 3.502A pdb=" N ALA C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 107 removed outlier: 3.761A pdb=" N MET C 107 " --> pdb=" O GLN C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 132 removed outlier: 3.512A pdb=" N LEU C 131 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 156 removed outlier: 3.940A pdb=" N ARG C 149 " --> pdb=" O ASP C 145 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 151 " --> pdb=" O ASN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.569A pdb=" N LYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 202 removed outlier: 3.544A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.558A pdb=" N ARG C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 242 removed outlier: 3.501A pdb=" N ILE C 234 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 256 removed outlier: 3.754A pdb=" N MET C 250 " --> pdb=" O GLY C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 284 through 289 Processing helix chain 'C' and resid 323 through 332 removed outlier: 3.693A pdb=" N GLU C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 43 removed outlier: 3.621A pdb=" N LEU E 25 " --> pdb=" O THR E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.502A pdb=" N ALA E 58 " --> pdb=" O PHE E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 107 removed outlier: 3.761A pdb=" N MET E 107 " --> pdb=" O GLN E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 132 removed outlier: 3.512A pdb=" N LEU E 131 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG E 132 " --> pdb=" O LEU E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 156 removed outlier: 3.939A pdb=" N ARG E 149 " --> pdb=" O ASP E 145 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS E 150 " --> pdb=" O GLU E 146 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS E 151 " --> pdb=" O ASN E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 173 removed outlier: 3.569A pdb=" N LYS E 172 " --> pdb=" O SER E 168 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA E 173 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 202 removed outlier: 3.544A pdb=" N ILE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.559A pdb=" N ARG E 221 " --> pdb=" O ILE E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 242 removed outlier: 3.502A pdb=" N ILE E 234 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 256 removed outlier: 3.755A pdb=" N MET E 250 " --> pdb=" O GLY E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 284 Processing helix chain 'E' and resid 284 through 289 Processing helix chain 'E' and resid 323 through 332 removed outlier: 3.693A pdb=" N GLU E 328 " --> pdb=" O PRO E 324 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG E 329 " --> pdb=" O GLU E 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 43 removed outlier: 3.621A pdb=" N LEU G 25 " --> pdb=" O THR G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 58 removed outlier: 3.501A pdb=" N ALA G 58 " --> pdb=" O PHE G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 107 removed outlier: 3.760A pdb=" N MET G 107 " --> pdb=" O GLN G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 132 removed outlier: 3.512A pdb=" N LEU G 131 " --> pdb=" O THR G 127 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG G 132 " --> pdb=" O LEU G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 156 removed outlier: 3.939A pdb=" N ARG G 149 " --> pdb=" O ASP G 145 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS G 151 " --> pdb=" O ASN G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 173 removed outlier: 3.569A pdb=" N LYS G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA G 173 " --> pdb=" O ASP G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 202 removed outlier: 3.546A pdb=" N ILE G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 215 No H-bonds generated for 'chain 'G' and resid 213 through 215' Processing helix chain 'G' and resid 216 through 224 removed outlier: 3.559A pdb=" N ARG G 221 " --> pdb=" O ILE G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 242 removed outlier: 3.501A pdb=" N ILE G 234 " --> pdb=" O SER G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 256 removed outlier: 3.754A pdb=" N MET G 250 " --> pdb=" O GLY G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 284 Processing helix chain 'G' and resid 284 through 289 Processing helix chain 'G' and resid 323 through 332 removed outlier: 3.693A pdb=" N GLU G 328 " --> pdb=" O PRO G 324 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG G 329 " --> pdb=" O GLU G 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 131 Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 147 through 156 removed outlier: 4.328A pdb=" N LYS B 151 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 173 removed outlier: 3.612A pdb=" N LYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 202 Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 230 through 242 Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 279 through 284 removed outlier: 3.747A pdb=" N ASP B 284 " --> pdb=" O VAL B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 290 Processing helix chain 'B' and resid 323 through 334 removed outlier: 3.607A pdb=" N GLU B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 131 Processing helix chain 'D' and resid 132 through 134 No H-bonds generated for 'chain 'D' and resid 132 through 134' Processing helix chain 'D' and resid 147 through 156 removed outlier: 4.328A pdb=" N LYS D 151 " --> pdb=" O ASN D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 173 removed outlier: 3.613A pdb=" N LYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 173 " --> pdb=" O ASP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 202 Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 230 through 242 Processing helix chain 'D' and resid 247 through 256 Processing helix chain 'D' and resid 279 through 284 removed outlier: 3.747A pdb=" N ASP D 284 " --> pdb=" O VAL D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 290 Processing helix chain 'D' and resid 323 through 334 removed outlier: 3.607A pdb=" N GLU D 328 " --> pdb=" O PRO D 324 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 131 Processing helix chain 'F' and resid 132 through 134 No H-bonds generated for 'chain 'F' and resid 132 through 134' Processing helix chain 'F' and resid 147 through 156 removed outlier: 4.328A pdb=" N LYS F 151 " --> pdb=" O ASN F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 173 removed outlier: 3.613A pdb=" N LYS F 172 " --> pdb=" O SER F 168 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA F 173 " --> pdb=" O ASP F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 202 Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 216 through 224 Processing helix chain 'F' and resid 230 through 242 Processing helix chain 'F' and resid 247 through 256 Processing helix chain 'F' and resid 279 through 284 removed outlier: 3.747A pdb=" N ASP F 284 " --> pdb=" O VAL F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 290 Processing helix chain 'F' and resid 323 through 334 removed outlier: 3.608A pdb=" N GLU F 328 " --> pdb=" O PRO F 324 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 131 Processing helix chain 'H' and resid 132 through 134 No H-bonds generated for 'chain 'H' and resid 132 through 134' Processing helix chain 'H' and resid 147 through 156 removed outlier: 4.328A pdb=" N LYS H 151 " --> pdb=" O ASN H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 173 removed outlier: 3.612A pdb=" N LYS H 172 " --> pdb=" O SER H 168 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA H 173 " --> pdb=" O ASP H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 202 Processing helix chain 'H' and resid 213 through 215 No H-bonds generated for 'chain 'H' and resid 213 through 215' Processing helix chain 'H' and resid 216 through 224 Processing helix chain 'H' and resid 230 through 242 Processing helix chain 'H' and resid 247 through 256 Processing helix chain 'H' and resid 279 through 284 removed outlier: 3.747A pdb=" N ASP H 284 " --> pdb=" O VAL H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 290 Processing helix chain 'H' and resid 323 through 334 removed outlier: 3.607A pdb=" N GLU H 328 " --> pdb=" O PRO H 324 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG H 329 " --> pdb=" O GLU H 325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 6.259A pdb=" N VAL A 118 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU A 142 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE A 120 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.287A pdb=" N ILE A 317 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL A 296 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU A 319 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 158 through 161 removed outlier: 6.259A pdb=" N VAL C 118 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LEU C 142 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE C 120 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 263 through 268 removed outlier: 6.287A pdb=" N ILE C 317 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL C 296 " --> pdb=" O ILE C 317 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU C 319 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 158 through 161 removed outlier: 6.260A pdb=" N VAL E 118 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LEU E 142 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE E 120 " --> pdb=" O LEU E 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 263 through 268 removed outlier: 6.287A pdb=" N ILE E 317 " --> pdb=" O VAL E 296 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL E 296 " --> pdb=" O ILE E 317 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU E 319 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 158 through 161 removed outlier: 6.260A pdb=" N VAL G 118 " --> pdb=" O PHE G 140 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU G 142 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE G 120 " --> pdb=" O LEU G 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 263 through 268 removed outlier: 6.287A pdb=" N ILE G 317 " --> pdb=" O VAL G 296 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL G 296 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU G 319 " --> pdb=" O ILE G 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 158 through 161 removed outlier: 6.591A pdb=" N VAL B 118 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU B 142 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE B 120 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL B 181 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N GLU B 210 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL B 183 " --> pdb=" O GLU B 210 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 263 through 268 removed outlier: 3.520A pdb=" N ARG B 263 " --> pdb=" O GLY B 322 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 322 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE B 321 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE B 293 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 158 through 161 removed outlier: 6.592A pdb=" N VAL D 118 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU D 142 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE D 120 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL D 181 " --> pdb=" O ILE D 208 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N GLU D 210 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL D 183 " --> pdb=" O GLU D 210 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 263 through 268 removed outlier: 3.521A pdb=" N ARG D 263 " --> pdb=" O GLY D 322 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY D 322 " --> pdb=" O ARG D 263 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE D 321 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE D 293 " --> pdb=" O ILE D 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 158 through 161 removed outlier: 6.592A pdb=" N VAL F 118 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU F 142 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE F 120 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL F 181 " --> pdb=" O ILE F 208 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N GLU F 210 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL F 183 " --> pdb=" O GLU F 210 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 263 through 268 removed outlier: 3.521A pdb=" N ARG F 263 " --> pdb=" O GLY F 322 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY F 322 " --> pdb=" O ARG F 263 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE F 321 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE F 293 " --> pdb=" O ILE F 321 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 158 through 161 removed outlier: 6.592A pdb=" N VAL H 118 " --> pdb=" O PHE H 140 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU H 142 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE H 120 " --> pdb=" O LEU H 142 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL H 181 " --> pdb=" O ILE H 208 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N GLU H 210 " --> pdb=" O VAL H 181 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL H 183 " --> pdb=" O GLU H 210 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 263 through 268 removed outlier: 3.521A pdb=" N ARG H 263 " --> pdb=" O GLY H 322 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY H 322 " --> pdb=" O ARG H 263 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE H 321 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE H 293 " --> pdb=" O ILE H 321 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2352 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: 3.11 Time building geometry restraints manager: 2.18 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: 5601 1.34 - 1.45: 1781 1.45 - 1.57: 9706 1.57 - 1.69: 4 1.69 - 1.80: 116 Bond restraints: 17208 Sorted by residual: bond pdb=" O12 PGW E 401 " pdb=" P PGW E 401 " ideal model delta sigma weight residual 1.636 1.693 -0.057 2.00e-02 2.50e+03 7.99e+00 bond pdb=" O12 PGW C 401 " pdb=" P PGW C 401 " ideal model delta sigma weight residual 1.636 1.693 -0.057 2.00e-02 2.50e+03 7.98e+00 bond pdb=" O12 PGW A 401 " pdb=" P PGW A 401 " ideal model delta sigma weight residual 1.636 1.692 -0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" O12 PGW G 401 " pdb=" P PGW G 401 " ideal model delta sigma weight residual 1.636 1.692 -0.056 2.00e-02 2.50e+03 7.88e+00 bond pdb=" C01 YQ1 A 402 " pdb=" N01 YQ1 A 402 " ideal model delta sigma weight residual 1.524 1.468 0.056 2.00e-02 2.50e+03 7.78e+00 ... (remaining 17203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 22546 1.43 - 2.86: 530 2.86 - 4.28: 97 4.28 - 5.71: 40 5.71 - 7.14: 25 Bond angle restraints: 23238 Sorted by residual: angle pdb=" C SER A 273 " pdb=" N LYS A 274 " pdb=" CA LYS A 274 " ideal model delta sigma weight residual 121.54 126.20 -4.66 1.91e+00 2.74e-01 5.94e+00 angle pdb=" C SER E 273 " pdb=" N LYS E 274 " pdb=" CA LYS E 274 " ideal model delta sigma weight residual 121.54 126.19 -4.65 1.91e+00 2.74e-01 5.94e+00 angle pdb=" C SER C 273 " pdb=" N LYS C 274 " pdb=" CA LYS C 274 " ideal model delta sigma weight residual 121.54 126.19 -4.65 1.91e+00 2.74e-01 5.91e+00 angle pdb=" C SER G 273 " pdb=" N LYS G 274 " pdb=" CA LYS G 274 " ideal model delta sigma weight residual 121.54 126.17 -4.63 1.91e+00 2.74e-01 5.87e+00 angle pdb=" O13 PGW E 401 " pdb=" P PGW E 401 " pdb=" O14 PGW E 401 " ideal model delta sigma weight residual 119.81 126.95 -7.14 3.00e+00 1.11e-01 5.66e+00 ... (remaining 23233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.41: 10363 28.41 - 56.82: 113 56.82 - 85.22: 16 85.22 - 113.63: 0 113.63 - 142.04: 12 Dihedral angle restraints: 10504 sinusoidal: 4352 harmonic: 6152 Sorted by residual: dihedral pdb=" C03 PGW C 401 " pdb=" C01 PGW C 401 " pdb=" C02 PGW C 401 " pdb=" O03 PGW C 401 " ideal model delta sinusoidal sigma weight residual 295.35 153.31 142.04 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C03 PGW A 401 " pdb=" C01 PGW A 401 " pdb=" C02 PGW A 401 " pdb=" O03 PGW A 401 " ideal model delta sinusoidal sigma weight residual 295.35 153.32 142.03 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C03 PGW E 401 " pdb=" C01 PGW E 401 " pdb=" C02 PGW E 401 " pdb=" O03 PGW E 401 " ideal model delta sinusoidal sigma weight residual 295.35 153.36 141.99 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 10501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1626 0.038 - 0.077: 700 0.077 - 0.115: 303 0.115 - 0.153: 59 0.153 - 0.191: 4 Chirality restraints: 2692 Sorted by residual: chirality pdb=" CA PHE G 88 " pdb=" N PHE G 88 " pdb=" C PHE G 88 " pdb=" CB PHE G 88 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.15e-01 chirality pdb=" CA PHE C 88 " pdb=" N PHE C 88 " pdb=" C PHE C 88 " pdb=" CB PHE C 88 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" CA PHE E 88 " pdb=" N PHE E 88 " pdb=" C PHE E 88 " pdb=" CB PHE E 88 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.95e-01 ... (remaining 2689 not shown) Planarity restraints: 3004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 47 " -0.034 2.00e-02 2.50e+03 6.72e-02 4.52e+01 pdb=" C THR C 47 " 0.116 2.00e-02 2.50e+03 pdb=" O THR C 47 " -0.043 2.00e-02 2.50e+03 pdb=" N VAL C 48 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 47 " 0.034 2.00e-02 2.50e+03 6.72e-02 4.51e+01 pdb=" C THR A 47 " -0.116 2.00e-02 2.50e+03 pdb=" O THR A 47 " 0.043 2.00e-02 2.50e+03 pdb=" N VAL A 48 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 47 " -0.034 2.00e-02 2.50e+03 6.72e-02 4.51e+01 pdb=" C THR E 47 " 0.116 2.00e-02 2.50e+03 pdb=" O THR E 47 " -0.043 2.00e-02 2.50e+03 pdb=" N VAL E 48 " -0.039 2.00e-02 2.50e+03 ... (remaining 3001 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 5026 2.83 - 3.41: 17605 3.41 - 3.99: 30081 3.99 - 4.56: 42504 4.56 - 5.14: 65028 Nonbonded interactions: 160244 Sorted by model distance: nonbonded pdb=" OE1 GLU C 133 " pdb=" OG SER D 240 " model vdw 2.255 3.040 nonbonded pdb=" OE1 GLU A 133 " pdb=" OG SER B 240 " model vdw 2.295 3.040 nonbonded pdb=" OE1 GLU E 133 " pdb=" OG SER F 240 " model vdw 2.301 3.040 nonbonded pdb=" OG SER B 279 " pdb=" OD1 ASP B 282 " model vdw 2.331 3.040 nonbonded pdb=" NH2 ARG E 308 " pdb=" OD2 ASP F 287 " model vdw 2.331 3.120 ... (remaining 160239 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 20 through 401) selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 16.830 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 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:9.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 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 : 0.006 0.057 17208 Z= 0.288 Angle : 0.617 7.139 23238 Z= 0.327 Chirality : 0.050 0.191 2692 Planarity : 0.007 0.067 3004 Dihedral : 10.715 142.041 6552 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.43 % Allowed : 2.39 % Favored : 97.17 % 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: 0.08 (0.18), residues: 2140 helix: 0.12 (0.16), residues: 1028 sheet: 3.16 (0.26), residues: 344 loop : -1.49 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 221 TYR 0.015 0.002 TYR G 247 PHE 0.010 0.002 PHE C 88 TRP 0.013 0.002 TRP C 52 HIS 0.004 0.001 HIS F 117 Details of bonding type rmsd covalent geometry : bond 0.00630 (17208) covalent geometry : angle 0.61708 (23238) hydrogen bonds : bond 0.20885 ( 816) hydrogen bonds : angle 6.82121 ( 2352) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 317 time to evaluate : 0.721 Fit side-chains REVERT: A 53 THR cc_start: 0.8572 (m) cc_final: 0.8261 (p) REVERT: C 53 THR cc_start: 0.8543 (m) cc_final: 0.8329 (p) REVERT: G 53 THR cc_start: 0.8542 (m) cc_final: 0.8335 (p) outliers start: 8 outliers final: 2 residues processed: 321 average time/residue: 0.8680 time to fit residues: 300.1929 Evaluate side-chains 148 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 248 GLU Chi-restraints excluded: chain H residue 248 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 HIS D 161 HIS F 161 HIS H 161 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.107302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.073015 restraints weight = 30444.678| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.84 r_work: 0.2895 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17208 Z= 0.146 Angle : 0.563 9.180 23238 Z= 0.291 Chirality : 0.047 0.235 2692 Planarity : 0.003 0.034 3004 Dihedral : 12.461 146.053 2546 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.99 % Allowed : 10.65 % Favored : 86.36 % 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: 0.52 (0.18), residues: 2140 helix: 0.86 (0.16), residues: 1052 sheet: 2.89 (0.26), residues: 320 loop : -1.56 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 241 TYR 0.017 0.001 TYR G 33 PHE 0.010 0.001 PHE C 88 TRP 0.006 0.001 TRP A 52 HIS 0.004 0.001 HIS C 39 Details of bonding type rmsd covalent geometry : bond 0.00320 (17208) covalent geometry : angle 0.56309 (23238) hydrogen bonds : bond 0.04556 ( 816) hydrogen bonds : angle 4.99180 ( 2352) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 180 time to evaluate : 0.441 Fit side-chains REVERT: A 73 MET cc_start: 0.4788 (OUTLIER) cc_final: 0.4322 (mpt) REVERT: A 222 MET cc_start: 0.8107 (tmt) cc_final: 0.7884 (tmm) REVERT: C 73 MET cc_start: 0.4643 (OUTLIER) cc_final: 0.4138 (mpt) REVERT: C 222 MET cc_start: 0.8109 (tmt) cc_final: 0.7869 (tmm) REVERT: G 33 TYR cc_start: 0.7371 (t80) cc_final: 0.6979 (t80) REVERT: G 53 THR cc_start: 0.8501 (m) cc_final: 0.8078 (p) REVERT: G 73 MET cc_start: 0.4702 (OUTLIER) cc_final: 0.4228 (mpt) REVERT: G 222 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8254 (tmt) REVERT: B 325 GLU cc_start: 0.8447 (mp0) cc_final: 0.8011 (tp30) REVERT: D 325 GLU cc_start: 0.8442 (mp0) cc_final: 0.8215 (tm-30) REVERT: F 222 MET cc_start: 0.8630 (mtt) cc_final: 0.8422 (mtp) REVERT: H 325 GLU cc_start: 0.8446 (mp0) cc_final: 0.8210 (tm-30) outliers start: 55 outliers final: 6 residues processed: 207 average time/residue: 0.5915 time to fit residues: 136.1347 Evaluate side-chains 165 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 222 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 0.0000 chunk 166 optimal weight: 4.9990 chunk 185 optimal weight: 0.0870 chunk 147 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.2168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.104536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.070199 restraints weight = 31154.431| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.91 r_work: 0.2805 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17208 Z= 0.131 Angle : 0.499 8.145 23238 Z= 0.263 Chirality : 0.046 0.183 2692 Planarity : 0.003 0.027 3004 Dihedral : 11.641 144.087 2540 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.66 % Allowed : 12.17 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.87 (0.18), residues: 2140 helix: 1.38 (0.16), residues: 1028 sheet: 2.68 (0.26), residues: 320 loop : -1.49 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 241 TYR 0.021 0.001 TYR A 33 PHE 0.022 0.001 PHE A 75 TRP 0.002 0.000 TRP A 123 HIS 0.003 0.001 HIS H 117 Details of bonding type rmsd covalent geometry : bond 0.00296 (17208) covalent geometry : angle 0.49869 (23238) hydrogen bonds : bond 0.04479 ( 816) hydrogen bonds : angle 4.64408 ( 2352) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 170 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.4542 (OUTLIER) cc_final: 0.4041 (mpt) REVERT: A 172 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8400 (tppt) REVERT: C 65 TYR cc_start: 0.7518 (m-80) cc_final: 0.7239 (m-80) REVERT: C 73 MET cc_start: 0.4636 (OUTLIER) cc_final: 0.4171 (mpt) REVERT: C 172 LYS cc_start: 0.8588 (tppt) cc_final: 0.8328 (tppt) REVERT: E 172 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8420 (tppt) REVERT: E 222 MET cc_start: 0.8938 (tpp) cc_final: 0.8644 (mmm) REVERT: G 53 THR cc_start: 0.8412 (m) cc_final: 0.8028 (p) REVERT: G 73 MET cc_start: 0.4565 (OUTLIER) cc_final: 0.4085 (mpt) REVERT: G 172 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8352 (tppt) REVERT: G 222 MET cc_start: 0.8968 (tpp) cc_final: 0.8666 (mmm) REVERT: G 274 LYS cc_start: 0.8784 (ptpt) cc_final: 0.8437 (ptpp) REVERT: B 116 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7957 (ttm-80) REVERT: B 239 MET cc_start: 0.8952 (mtt) cc_final: 0.8701 (mtt) REVERT: B 310 TYR cc_start: 0.7846 (t80) cc_final: 0.7645 (t80) REVERT: B 325 GLU cc_start: 0.8495 (mp0) cc_final: 0.8056 (tp30) REVERT: D 116 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7974 (ttm-80) REVERT: D 239 MET cc_start: 0.8943 (mtt) cc_final: 0.8687 (mtt) REVERT: D 325 GLU cc_start: 0.8479 (mp0) cc_final: 0.8256 (tm-30) REVERT: F 116 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7907 (ttm-80) REVERT: H 325 GLU cc_start: 0.8496 (mp0) cc_final: 0.8266 (tm-30) outliers start: 49 outliers final: 7 residues processed: 204 average time/residue: 0.7130 time to fit residues: 159.4893 Evaluate side-chains 162 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 172 LYS Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain F residue 116 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 56 optimal weight: 0.2980 chunk 29 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 54 optimal weight: 0.0170 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.105447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.071444 restraints weight = 31047.736| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.90 r_work: 0.2835 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17208 Z= 0.096 Angle : 0.468 6.848 23238 Z= 0.243 Chirality : 0.045 0.161 2692 Planarity : 0.003 0.021 3004 Dihedral : 11.292 141.371 2540 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.28 % Allowed : 12.93 % Favored : 84.78 % 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: 1.16 (0.18), residues: 2140 helix: 1.72 (0.16), residues: 1028 sheet: 2.60 (0.27), residues: 320 loop : -1.39 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 241 TYR 0.021 0.001 TYR A 33 PHE 0.009 0.001 PHE A 75 TRP 0.002 0.000 TRP E 123 HIS 0.001 0.000 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00204 (17208) covalent geometry : angle 0.46762 (23238) hydrogen bonds : bond 0.03228 ( 816) hydrogen bonds : angle 4.40133 ( 2352) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 164 time to evaluate : 0.725 Fit side-chains REVERT: A 73 MET cc_start: 0.4556 (OUTLIER) cc_final: 0.4071 (mpt) REVERT: C 65 TYR cc_start: 0.7552 (m-80) cc_final: 0.7275 (m-80) REVERT: C 73 MET cc_start: 0.4712 (OUTLIER) cc_final: 0.4197 (mpt) REVERT: C 103 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7595 (tp-100) REVERT: C 172 LYS cc_start: 0.8568 (tppt) cc_final: 0.8325 (tppt) REVERT: E 65 TYR cc_start: 0.7670 (m-80) cc_final: 0.7382 (m-80) REVERT: E 73 MET cc_start: 0.4978 (OUTLIER) cc_final: 0.4528 (mpt) REVERT: E 103 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7629 (tp-100) REVERT: E 172 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8326 (tppt) REVERT: E 222 MET cc_start: 0.8925 (tpp) cc_final: 0.8621 (mmm) REVERT: G 73 MET cc_start: 0.4607 (OUTLIER) cc_final: 0.4110 (mpt) REVERT: G 103 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7662 (tp-100) REVERT: G 172 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8285 (tppt) REVERT: G 222 MET cc_start: 0.8971 (tpp) cc_final: 0.8656 (mmm) REVERT: B 116 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7907 (ttm-80) REVERT: B 239 MET cc_start: 0.8926 (mtt) cc_final: 0.8681 (mtt) REVERT: B 325 GLU cc_start: 0.8512 (mp0) cc_final: 0.8098 (tp30) REVERT: D 116 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7921 (ttm-80) REVERT: D 239 MET cc_start: 0.8916 (mtt) cc_final: 0.8670 (mtt) REVERT: D 325 GLU cc_start: 0.8488 (mp0) cc_final: 0.8065 (tp30) REVERT: F 116 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7922 (ttm-80) REVERT: H 325 GLU cc_start: 0.8499 (mp0) cc_final: 0.8046 (tp30) outliers start: 42 outliers final: 11 residues processed: 187 average time/residue: 0.6318 time to fit residues: 129.9300 Evaluate side-chains 162 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 172 LYS Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 266 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 33 optimal weight: 20.0000 chunk 129 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 186 optimal weight: 8.9990 chunk 209 optimal weight: 0.0050 chunk 86 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN C 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.104371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.070284 restraints weight = 31100.086| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.90 r_work: 0.2800 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17208 Z= 0.108 Angle : 0.469 7.231 23238 Z= 0.246 Chirality : 0.045 0.155 2692 Planarity : 0.003 0.024 3004 Dihedral : 10.979 136.828 2540 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.72 % Allowed : 12.72 % Favored : 84.57 % 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: 1.38 (0.18), residues: 2140 helix: 1.86 (0.16), residues: 1028 sheet: 2.87 (0.26), residues: 312 loop : -1.26 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 241 TYR 0.009 0.001 TYR E 51 PHE 0.030 0.001 PHE C 54 TRP 0.003 0.000 TRP C 52 HIS 0.002 0.001 HIS F 117 Details of bonding type rmsd covalent geometry : bond 0.00240 (17208) covalent geometry : angle 0.46940 (23238) hydrogen bonds : bond 0.03538 ( 816) hydrogen bonds : angle 4.35545 ( 2352) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 155 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.4626 (OUTLIER) cc_final: 0.4135 (mpt) REVERT: A 103 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7732 (tp-100) REVERT: A 274 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8453 (ptpp) REVERT: C 65 TYR cc_start: 0.7616 (m-80) cc_final: 0.7211 (m-80) REVERT: C 103 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7731 (tp-100) REVERT: C 172 LYS cc_start: 0.8655 (tppt) cc_final: 0.8434 (tppt) REVERT: E 73 MET cc_start: 0.4911 (OUTLIER) cc_final: 0.4505 (mpt) REVERT: E 103 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7652 (tp-100) REVERT: E 172 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8442 (tppt) REVERT: E 222 MET cc_start: 0.8955 (tpp) cc_final: 0.8661 (mmm) REVERT: G 73 MET cc_start: 0.4567 (OUTLIER) cc_final: 0.4056 (mpt) REVERT: G 103 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7760 (tp-100) REVERT: G 172 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8455 (tppt) REVERT: G 222 MET cc_start: 0.8991 (tpp) cc_final: 0.8678 (mmm) REVERT: B 116 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7975 (ttm-80) REVERT: B 239 MET cc_start: 0.8934 (mtt) cc_final: 0.8677 (mtt) REVERT: B 325 GLU cc_start: 0.8532 (mp0) cc_final: 0.8103 (tp30) REVERT: D 116 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7993 (ttm-80) REVERT: D 172 LYS cc_start: 0.8841 (mtpp) cc_final: 0.8603 (mtpt) REVERT: D 239 MET cc_start: 0.8930 (mtt) cc_final: 0.8686 (mtt) REVERT: D 325 GLU cc_start: 0.8481 (mp0) cc_final: 0.8259 (tm-30) REVERT: F 116 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7995 (ttm-80) REVERT: H 172 LYS cc_start: 0.8834 (mtpp) cc_final: 0.8592 (mtpt) REVERT: H 274 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8720 (mtmm) REVERT: H 325 GLU cc_start: 0.8480 (mp0) cc_final: 0.8245 (tm-30) outliers start: 50 outliers final: 12 residues processed: 188 average time/residue: 0.7056 time to fit residues: 145.5879 Evaluate side-chains 159 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 172 LYS Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 150 LYS Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain H residue 274 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 204 optimal weight: 0.7980 chunk 177 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 144 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 163 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 211 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 332 ASN E 332 ASN G 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.103790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.069615 restraints weight = 30904.917| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.88 r_work: 0.2786 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17208 Z= 0.114 Angle : 0.467 7.171 23238 Z= 0.244 Chirality : 0.046 0.162 2692 Planarity : 0.003 0.026 3004 Dihedral : 10.801 133.977 2540 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.96 % Allowed : 13.97 % Favored : 84.08 % 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: 1.46 (0.19), residues: 2140 helix: 1.93 (0.17), residues: 1032 sheet: 2.93 (0.27), residues: 312 loop : -1.25 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 199 TYR 0.010 0.001 TYR C 51 PHE 0.011 0.001 PHE A 75 TRP 0.002 0.000 TRP C 52 HIS 0.004 0.001 HIS C 39 Details of bonding type rmsd covalent geometry : bond 0.00260 (17208) covalent geometry : angle 0.46685 (23238) hydrogen bonds : bond 0.03502 ( 816) hydrogen bonds : angle 4.31180 ( 2352) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 153 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7809 (tp-100) REVERT: A 274 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8499 (ptpp) REVERT: C 65 TYR cc_start: 0.7711 (m-80) cc_final: 0.7296 (m-80) REVERT: C 103 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7806 (tp-100) REVERT: C 172 LYS cc_start: 0.8637 (tppt) cc_final: 0.8415 (tppt) REVERT: E 73 MET cc_start: 0.4920 (OUTLIER) cc_final: 0.4470 (mpt) REVERT: E 103 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7784 (tp-100) REVERT: E 172 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8473 (tppt) REVERT: E 222 MET cc_start: 0.8956 (tpp) cc_final: 0.8662 (mmm) REVERT: G 103 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7786 (tp-100) REVERT: G 172 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8458 (tppt) REVERT: G 222 MET cc_start: 0.8985 (tpp) cc_final: 0.8679 (mmm) REVERT: B 116 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.8018 (ttm-80) REVERT: B 239 MET cc_start: 0.8954 (mtt) cc_final: 0.8726 (mtt) REVERT: B 325 GLU cc_start: 0.8610 (mp0) cc_final: 0.8144 (tp30) REVERT: D 116 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.8055 (ttm-80) REVERT: D 239 MET cc_start: 0.8954 (mtt) cc_final: 0.8707 (mtt) REVERT: D 325 GLU cc_start: 0.8530 (mp0) cc_final: 0.7662 (tm-30) REVERT: F 116 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.8104 (ttm-80) REVERT: H 325 GLU cc_start: 0.8538 (mp0) cc_final: 0.7654 (tm-30) outliers start: 36 outliers final: 12 residues processed: 178 average time/residue: 0.7771 time to fit residues: 149.9019 Evaluate side-chains 153 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 172 LYS Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 150 LYS Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain H residue 274 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 154 optimal weight: 2.9990 chunk 189 optimal weight: 0.9980 chunk 152 optimal weight: 0.3980 chunk 104 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 4 optimal weight: 0.0270 chunk 50 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.0440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 332 ASN E 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.103649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.069487 restraints weight = 30817.636| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.87 r_work: 0.2790 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17208 Z= 0.114 Angle : 0.490 9.820 23238 Z= 0.251 Chirality : 0.046 0.161 2692 Planarity : 0.003 0.028 3004 Dihedral : 10.752 133.067 2540 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.58 % Allowed : 14.51 % Favored : 83.91 % 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: 1.45 (0.19), residues: 2140 helix: 1.93 (0.17), residues: 1032 sheet: 2.95 (0.27), residues: 312 loop : -1.28 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 241 TYR 0.008 0.001 TYR A 51 PHE 0.028 0.001 PHE C 54 TRP 0.003 0.000 TRP E 52 HIS 0.004 0.001 HIS C 39 Details of bonding type rmsd covalent geometry : bond 0.00258 (17208) covalent geometry : angle 0.49044 (23238) hydrogen bonds : bond 0.03515 ( 816) hydrogen bonds : angle 4.27922 ( 2352) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7845 (tp-100) REVERT: A 172 LYS cc_start: 0.8790 (tppt) cc_final: 0.8458 (ttmm) REVERT: A 274 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8521 (ptpp) REVERT: C 65 TYR cc_start: 0.7745 (m-80) cc_final: 0.7318 (m-80) REVERT: C 103 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7824 (tp-100) REVERT: C 172 LYS cc_start: 0.8690 (tppt) cc_final: 0.8471 (tppt) REVERT: E 103 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7799 (tp-100) REVERT: E 172 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8426 (tppt) REVERT: E 222 MET cc_start: 0.8975 (tpp) cc_final: 0.8668 (mmm) REVERT: G 103 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7846 (tp-100) REVERT: G 172 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8440 (tppt) REVERT: G 222 MET cc_start: 0.8982 (tpp) cc_final: 0.8679 (mmm) REVERT: B 116 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8070 (ttm-80) REVERT: B 239 MET cc_start: 0.8932 (mtt) cc_final: 0.8701 (mtt) REVERT: D 116 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8102 (ttm-80) REVERT: D 172 LYS cc_start: 0.8838 (mtpp) cc_final: 0.8608 (mtpt) REVERT: D 239 MET cc_start: 0.8925 (mtt) cc_final: 0.8693 (mtt) REVERT: F 116 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8113 (ttm-80) REVERT: H 172 LYS cc_start: 0.8824 (mtpp) cc_final: 0.8592 (mtpt) outliers start: 29 outliers final: 13 residues processed: 170 average time/residue: 0.7519 time to fit residues: 138.5930 Evaluate side-chains 153 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 172 LYS Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 266 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- 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: 69.5327 > 50: distance: 11 - 15: 26.190 distance: 15 - 16: 32.883 distance: 16 - 17: 19.523 distance: 16 - 19: 29.627 distance: 17 - 18: 28.184 distance: 17 - 24: 21.187 distance: 19 - 20: 39.874 distance: 20 - 21: 13.325 distance: 21 - 22: 25.331 distance: 22 - 23: 21.218 distance: 24 - 25: 16.051 distance: 25 - 26: 30.787 distance: 25 - 28: 9.913 distance: 26 - 27: 39.387 distance: 26 - 32: 19.105 distance: 28 - 29: 29.045 distance: 29 - 30: 26.452 distance: 29 - 31: 42.101 distance: 32 - 33: 15.104 distance: 33 - 34: 46.882 distance: 33 - 36: 38.504 distance: 34 - 41: 15.978 distance: 36 - 37: 18.759 distance: 37 - 38: 30.420 distance: 38 - 39: 17.665 distance: 38 - 40: 22.931 distance: 41 - 42: 26.215 distance: 42 - 43: 28.731 distance: 43 - 44: 25.042 distance: 43 - 45: 22.073 distance: 45 - 46: 18.088 distance: 46 - 47: 30.304 distance: 46 - 49: 28.817 distance: 47 - 48: 10.046 distance: 47 - 52: 34.914 distance: 49 - 50: 33.693 distance: 49 - 51: 31.815 distance: 52 - 53: 17.693 distance: 53 - 54: 11.365 distance: 53 - 56: 41.018 distance: 54 - 55: 7.515 distance: 54 - 58: 36.668 distance: 55 - 81: 49.801 distance: 56 - 57: 6.020 distance: 58 - 59: 14.317 distance: 59 - 60: 35.437 distance: 59 - 62: 17.763 distance: 60 - 61: 33.406 distance: 60 - 65: 5.999 distance: 62 - 63: 22.990 distance: 62 - 64: 21.275 distance: 65 - 66: 7.535 distance: 66 - 67: 24.597 distance: 66 - 69: 37.501 distance: 67 - 68: 33.553 distance: 67 - 73: 22.755 distance: 69 - 70: 27.602 distance: 70 - 71: 13.786 distance: 70 - 72: 15.768 distance: 73 - 74: 32.126 distance: 74 - 75: 16.442 distance: 74 - 77: 28.924 distance: 75 - 76: 18.340 distance: 75 - 81: 22.215 distance: 77 - 78: 31.167 distance: 78 - 79: 15.226 distance: 78 - 80: 22.095 distance: 81 - 82: 21.443 distance: 82 - 83: 15.732 distance: 82 - 85: 26.323 distance: 83 - 84: 31.875 distance: 83 - 86: 27.903