Starting phenix.real_space_refine on Sat May 2 17:47:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jer_36193/05_2026/8jer_36193.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jer_36193/05_2026/8jer_36193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jer_36193/05_2026/8jer_36193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jer_36193/05_2026/8jer_36193.map" model { file = "/net/cci-nas-00/data/ceres_data/8jer_36193/05_2026/8jer_36193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jer_36193/05_2026/8jer_36193.cif" } resolution = 3.45 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= 0.030 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 45 5.16 5 C 5008 2.51 5 N 1384 2.21 5 O 1470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7907 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1531 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 4, 'TRANS': 201} Chain breaks: 2 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 7, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 2396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2396 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 10, 'GLN:plan1': 3, 'ARG:plan': 7, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 114 Chain: "R" Number of atoms: 1927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 1927 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 277} Chain breaks: 2 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 601 Unresolved non-hydrogen dihedrals: 406 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'ASP:plan': 9, 'HIS:plan': 3, 'PHE:plan': 14, 'GLU:plan': 5, 'ASN:plan1': 6, 'ARG:plan': 8, 'TRP:plan': 4, 'GLN:plan1': 5, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 267 Chain: "G" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 384 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1658 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 53 Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'OJX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.21, per 1000 atoms: 0.28 Number of scatterers: 7907 At special positions: 0 Unit cell: (132.797, 120.725, 87.8, 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 45 16.00 O 1470 8.00 N 1384 7.00 C 5008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 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: 0.56 Conformation dependent library (CDL) restraints added in 517.2 milliseconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2090 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 14 sheets defined 35.7% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 removed outlier: 3.777A pdb=" N LYS A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.530A pdb=" N LYS A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 removed outlier: 3.735A pdb=" N ASN A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.568A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.699A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 52 removed outlier: 3.943A pdb=" N LYS R 28 " --> pdb=" O ASP R 24 " (cutoff:3.500A) Proline residue: R 31 - end of helix removed outlier: 3.821A pdb=" N LEU R 47 " --> pdb=" O LEU R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 89 removed outlier: 3.508A pdb=" N LEU R 80 " --> pdb=" O LEU R 76 " (cutoff:3.500A) Proline residue: R 81 - end of helix removed outlier: 3.537A pdb=" N ASN R 86 " --> pdb=" O PHE R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 130 Processing helix chain 'R' and resid 134 through 139 Processing helix chain 'R' and resid 140 through 160 Processing helix chain 'R' and resid 161 through 163 No H-bonds generated for 'chain 'R' and resid 161 through 163' Processing helix chain 'R' and resid 187 through 218 removed outlier: 3.820A pdb=" N ALA R 191 " --> pdb=" O GLN R 187 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Proline residue: R 200 - end of helix Processing helix chain 'R' and resid 226 through 262 removed outlier: 3.736A pdb=" N ALA R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 268 through 290 removed outlier: 4.160A pdb=" N VAL R 272 " --> pdb=" O VAL R 268 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE R 277 " --> pdb=" O ASP R 273 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR R 283 " --> pdb=" O THR R 279 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR R 284 " --> pdb=" O LEU R 280 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER R 287 " --> pdb=" O THR R 283 " (cutoff:3.500A) Processing helix chain 'R' and resid 290 through 295 removed outlier: 3.622A pdb=" N TYR R 294 " --> pdb=" O ASP R 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.665A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.669A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'H' and resid 220 through 224 removed outlier: 4.203A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191 removed outlier: 6.364A pdb=" N VAL A 34 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N PHE A 200 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU A 36 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N ALA A 221 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ASP A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.510A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.652A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.070A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.590A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.692A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.694A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.252A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 11 through 12 Processing sheet with id=AB1, first strand: chain 'R' and resid 170 through 171 removed outlier: 3.598A pdb=" N ALA R 174 " --> pdb=" O ASN R 171 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.968A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR H 118 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 155 through 159 removed outlier: 3.950A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR H 213 " --> pdb=" O SER H 206 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 194 through 195 removed outlier: 5.556A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) 393 hydrogen bonds defined for protein. 1104 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: 1.21 Time building geometry restraints manager: 0.82 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: 2622 1.34 - 1.46: 1819 1.46 - 1.58: 3570 1.58 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 8069 Sorted by residual: bond pdb=" C LYS R 15 " pdb=" N LYS R 16 " ideal model delta sigma weight residual 1.331 1.233 0.098 1.30e-02 5.92e+03 5.72e+01 bond pdb=" CA ILE R 98 " pdb=" CB ILE R 98 " ideal model delta sigma weight residual 1.539 1.521 0.018 5.40e-03 3.43e+04 1.15e+01 bond pdb=" C06 OJX R 401 " pdb=" N04 OJX R 401 " ideal model delta sigma weight residual 1.382 1.322 0.060 2.00e-02 2.50e+03 8.92e+00 bond pdb=" N GLY R 173 " pdb=" CA GLY R 173 " ideal model delta sigma weight residual 1.446 1.484 -0.038 1.33e-02 5.65e+03 8.30e+00 bond pdb=" C07 OJX R 401 " pdb=" N04 OJX R 401 " ideal model delta sigma weight residual 1.370 1.318 0.052 2.00e-02 2.50e+03 6.70e+00 ... (remaining 8064 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 10816 1.99 - 3.99: 157 3.99 - 5.98: 33 5.98 - 7.97: 5 7.97 - 9.97: 4 Bond angle restraints: 11015 Sorted by residual: angle pdb=" N PRO R 31 " pdb=" CA PRO R 31 " pdb=" C PRO R 31 " ideal model delta sigma weight residual 110.70 117.41 -6.71 1.22e+00 6.72e-01 3.02e+01 angle pdb=" CA PRO R 31 " pdb=" C PRO R 31 " pdb=" N PRO R 32 " ideal model delta sigma weight residual 117.93 123.45 -5.52 1.20e+00 6.94e-01 2.12e+01 angle pdb=" N TYR R 284 " pdb=" CA TYR R 284 " pdb=" C TYR R 284 " ideal model delta sigma weight residual 111.36 106.58 4.78 1.09e+00 8.42e-01 1.92e+01 angle pdb=" N VAL H 64 " pdb=" CA VAL H 64 " pdb=" C VAL H 64 " ideal model delta sigma weight residual 113.71 109.62 4.09 9.50e-01 1.11e+00 1.85e+01 angle pdb=" CA LYS R 15 " pdb=" C LYS R 15 " pdb=" N LYS R 16 " ideal model delta sigma weight residual 116.21 110.75 5.46 1.29e+00 6.01e-01 1.79e+01 ... (remaining 11010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 4282 17.00 - 34.00: 338 34.00 - 51.00: 67 51.00 - 68.00: 5 68.00 - 85.00: 5 Dihedral angle restraints: 4697 sinusoidal: 1466 harmonic: 3231 Sorted by residual: dihedral pdb=" CB CYS R 19 " pdb=" SG CYS R 19 " pdb=" SG CYS R 266 " pdb=" CB CYS R 266 " ideal model delta sinusoidal sigma weight residual 93.00 171.24 -78.24 1 1.00e+01 1.00e-02 7.64e+01 dihedral pdb=" CB CYS R 100 " pdb=" SG CYS R 100 " pdb=" SG CYS R 177 " pdb=" CB CYS R 177 " ideal model delta sinusoidal sigma weight residual 93.00 123.58 -30.58 1 1.00e+01 1.00e-02 1.34e+01 dihedral pdb=" CA ASP B 258 " pdb=" C ASP B 258 " pdb=" N GLN B 259 " pdb=" CA GLN B 259 " ideal model delta harmonic sigma weight residual 180.00 163.88 16.12 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 4694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1044 0.053 - 0.106: 212 0.106 - 0.159: 33 0.159 - 0.211: 1 0.211 - 0.264: 2 Chirality restraints: 1292 Sorted by residual: chirality pdb=" CB ILE R 182 " pdb=" CA ILE R 182 " pdb=" CG1 ILE R 182 " pdb=" CG2 ILE R 182 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA PRO R 31 " pdb=" N PRO R 31 " pdb=" C PRO R 31 " pdb=" CB PRO R 31 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB THR H 91 " pdb=" CA THR H 91 " pdb=" OG1 THR H 91 " pdb=" CG2 THR H 91 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.32e-01 ... (remaining 1289 not shown) Planarity restraints: 1423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN R 170 " 0.023 2.00e-02 2.50e+03 4.62e-02 2.14e+01 pdb=" C GLN R 170 " -0.080 2.00e-02 2.50e+03 pdb=" O GLN R 170 " 0.031 2.00e-02 2.50e+03 pdb=" N ASN R 171 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP R 290 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO R 291 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO R 291 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 291 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 14 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C ASP R 14 " -0.034 2.00e-02 2.50e+03 pdb=" O ASP R 14 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS R 15 " 0.011 2.00e-02 2.50e+03 ... (remaining 1420 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 902 2.75 - 3.29: 7747 3.29 - 3.82: 12647 3.82 - 4.36: 14004 4.36 - 4.90: 25956 Nonbonded interactions: 61256 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.211 3.040 nonbonded pdb=" O LEU R 66 " pdb=" OH TYR R 294 " model vdw 2.223 3.040 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.242 3.040 nonbonded pdb=" O ARG H 67 " pdb=" OG1 THR H 84 " model vdw 2.267 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.285 3.040 ... (remaining 61251 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.160 Find NCS groups from input model: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 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 : 0.004 0.098 8074 Z= 0.207 Angle : 0.630 9.966 11025 Z= 0.358 Chirality : 0.044 0.264 1292 Planarity : 0.004 0.049 1423 Dihedral : 12.883 85.002 2592 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.14 % Allowed : 0.28 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 are not related in a simple way. whole: 0.23 (0.27), residues: 1097 helix: 1.74 (0.29), residues: 352 sheet: -1.14 (0.31), residues: 283 loop : -0.08 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 18 TYR 0.013 0.001 TYR H 190 PHE 0.012 0.001 PHE B 151 TRP 0.007 0.001 TRP H 36 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 8069) covalent geometry : angle 0.62949 (11015) SS BOND : bond 0.00185 ( 5) SS BOND : angle 0.66337 ( 10) hydrogen bonds : bond 0.22468 ( 393) hydrogen bonds : angle 7.85760 ( 1104) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7160 (tm-30) cc_final: 0.6923 (tm-30) REVERT: A 208 GLU cc_start: 0.7168 (tp30) cc_final: 0.6643 (tt0) REVERT: B 273 ILE cc_start: 0.8113 (mp) cc_final: 0.7896 (mt) REVERT: R 109 MET cc_start: 0.6415 (tmm) cc_final: 0.6054 (ttp) REVERT: R 131 HIS cc_start: 0.8438 (m-70) cc_final: 0.8089 (m-70) REVERT: R 186 PHE cc_start: 0.6540 (OUTLIER) cc_final: 0.6268 (t80) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.0946 time to fit residues: 23.0096 Evaluate side-chains 142 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 186 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 347 ASN B 17 GLN R 175 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.196799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.146542 restraints weight = 9747.373| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.87 r_work: 0.3543 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8074 Z= 0.233 Angle : 0.613 10.614 11025 Z= 0.331 Chirality : 0.046 0.152 1292 Planarity : 0.004 0.068 1423 Dihedral : 4.232 45.636 1188 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.46 % Favored : 96.44 % Rotamer: Outliers : 1.97 % Allowed : 10.70 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 are not related in a simple way. whole: 0.14 (0.26), residues: 1097 helix: 1.96 (0.28), residues: 354 sheet: -1.22 (0.29), residues: 289 loop : -0.39 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 111 TYR 0.020 0.002 TYR H 190 PHE 0.017 0.002 PHE H 27 TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 8069) covalent geometry : angle 0.61276 (11015) SS BOND : bond 0.00433 ( 5) SS BOND : angle 0.82841 ( 10) hydrogen bonds : bond 0.04639 ( 393) hydrogen bonds : angle 5.27060 ( 1104) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.322 Fit side-chains REVERT: A 187 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7423 (tm-30) REVERT: A 208 GLU cc_start: 0.7834 (tp30) cc_final: 0.7062 (tt0) REVERT: B 59 TYR cc_start: 0.9093 (m-80) cc_final: 0.8701 (m-80) REVERT: B 273 ILE cc_start: 0.8744 (mp) cc_final: 0.8479 (mt) REVERT: R 109 MET cc_start: 0.6334 (tmm) cc_final: 0.5556 (ttp) REVERT: R 131 HIS cc_start: 0.8445 (m-70) cc_final: 0.7875 (m-70) REVERT: R 186 PHE cc_start: 0.6972 (OUTLIER) cc_final: 0.6702 (t80) REVERT: R 220 MET cc_start: 0.8449 (ptm) cc_final: 0.8081 (ptm) REVERT: H 18 ARG cc_start: 0.7609 (tpp80) cc_final: 0.7381 (ttm170) outliers start: 14 outliers final: 12 residues processed: 159 average time/residue: 0.0986 time to fit residues: 20.8413 Evaluate side-chains 153 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 186 PHE Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 63 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.193668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.139042 restraints weight = 9550.443| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.41 r_work: 0.3528 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8074 Z= 0.192 Angle : 0.547 7.004 11025 Z= 0.296 Chirality : 0.045 0.186 1292 Planarity : 0.004 0.056 1423 Dihedral : 4.078 46.004 1188 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.56 % Favored : 96.35 % Rotamer: Outliers : 3.24 % Allowed : 11.41 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 are not related in a simple way. whole: 0.08 (0.26), residues: 1097 helix: 2.04 (0.28), residues: 355 sheet: -1.30 (0.29), residues: 292 loop : -0.50 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 18 TYR 0.017 0.002 TYR H 190 PHE 0.016 0.002 PHE A 336 TRP 0.008 0.001 TRP H 36 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 8069) covalent geometry : angle 0.54683 (11015) SS BOND : bond 0.00353 ( 5) SS BOND : angle 0.78162 ( 10) hydrogen bonds : bond 0.04029 ( 393) hydrogen bonds : angle 4.86852 ( 1104) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.330 Fit side-chains REVERT: A 208 GLU cc_start: 0.7785 (tp30) cc_final: 0.7071 (tt0) REVERT: B 17 GLN cc_start: 0.7888 (pt0) cc_final: 0.7609 (pt0) REVERT: B 59 TYR cc_start: 0.8957 (m-80) cc_final: 0.8605 (m-80) REVERT: B 75 GLN cc_start: 0.8838 (mt0) cc_final: 0.8623 (mt0) REVERT: B 163 ASP cc_start: 0.8166 (p0) cc_final: 0.7955 (p0) REVERT: B 234 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8069 (m-10) REVERT: B 273 ILE cc_start: 0.8654 (mp) cc_final: 0.8428 (mt) REVERT: R 109 MET cc_start: 0.6346 (tmm) cc_final: 0.5974 (ttt) REVERT: R 131 HIS cc_start: 0.8481 (m-70) cc_final: 0.7962 (m-70) REVERT: R 186 PHE cc_start: 0.7039 (OUTLIER) cc_final: 0.6771 (t80) REVERT: R 220 MET cc_start: 0.8495 (ptm) cc_final: 0.8227 (ptm) REVERT: H 18 ARG cc_start: 0.7670 (tpp80) cc_final: 0.7241 (ttm170) outliers start: 23 outliers final: 17 residues processed: 167 average time/residue: 0.0909 time to fit residues: 20.5405 Evaluate side-chains 159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 186 PHE Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 87 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 86 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 32 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.194644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.140917 restraints weight = 9712.740| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.72 r_work: 0.3511 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8074 Z= 0.166 Angle : 0.523 7.021 11025 Z= 0.280 Chirality : 0.044 0.179 1292 Planarity : 0.004 0.064 1423 Dihedral : 3.982 45.951 1188 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.01 % Favored : 96.90 % Rotamer: Outliers : 4.08 % Allowed : 14.08 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 are not related in a simple way. whole: 0.13 (0.26), residues: 1097 helix: 2.14 (0.28), residues: 355 sheet: -1.34 (0.29), residues: 291 loop : -0.49 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 96 TYR 0.020 0.001 TYR A 297 PHE 0.014 0.001 PHE H 27 TRP 0.007 0.001 TRP H 36 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 8069) covalent geometry : angle 0.52234 (11015) SS BOND : bond 0.00370 ( 5) SS BOND : angle 0.68971 ( 10) hydrogen bonds : bond 0.03614 ( 393) hydrogen bonds : angle 4.61084 ( 1104) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7800 (tp30) cc_final: 0.7049 (tt0) REVERT: A 275 PHE cc_start: 0.9132 (t80) cc_final: 0.8853 (t80) REVERT: B 17 GLN cc_start: 0.8044 (pt0) cc_final: 0.7819 (pt0) REVERT: B 163 ASP cc_start: 0.8176 (p0) cc_final: 0.7871 (p0) REVERT: B 234 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8160 (m-10) REVERT: B 273 ILE cc_start: 0.8684 (mp) cc_final: 0.8452 (mt) REVERT: R 131 HIS cc_start: 0.8452 (m-70) cc_final: 0.7879 (m-70) REVERT: R 186 PHE cc_start: 0.7117 (OUTLIER) cc_final: 0.6821 (t80) REVERT: H 18 ARG cc_start: 0.7636 (tpp80) cc_final: 0.7128 (ttm170) outliers start: 29 outliers final: 21 residues processed: 167 average time/residue: 0.0892 time to fit residues: 20.4624 Evaluate side-chains 165 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 186 PHE Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 44 optimal weight: 0.9990 chunk 28 optimal weight: 0.0970 chunk 33 optimal weight: 0.7980 chunk 85 optimal weight: 0.0000 chunk 80 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 overall best weight: 0.4982 ------------------------------------------------------------------------------- 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 = 0.4316 r_free = 0.4316 target = 0.196802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.151983 restraints weight = 9577.078| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.42 r_work: 0.3551 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8074 Z= 0.122 Angle : 0.500 9.850 11025 Z= 0.267 Chirality : 0.043 0.175 1292 Planarity : 0.004 0.064 1423 Dihedral : 3.880 45.545 1188 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.83 % Favored : 97.08 % Rotamer: Outliers : 3.94 % Allowed : 15.21 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 are not related in a simple way. whole: 0.22 (0.26), residues: 1097 helix: 2.22 (0.28), residues: 355 sheet: -1.22 (0.30), residues: 284 loop : -0.50 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 46 TYR 0.019 0.001 TYR A 297 PHE 0.021 0.001 PHE H 68 TRP 0.007 0.001 TRP A 212 HIS 0.002 0.000 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8069) covalent geometry : angle 0.49948 (11015) SS BOND : bond 0.00337 ( 5) SS BOND : angle 0.71801 ( 10) hydrogen bonds : bond 0.03354 ( 393) hydrogen bonds : angle 4.41137 ( 1104) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7686 (tp30) cc_final: 0.7417 (tp30) REVERT: A 275 PHE cc_start: 0.9129 (t80) cc_final: 0.8906 (t80) REVERT: B 17 GLN cc_start: 0.7979 (pt0) cc_final: 0.7756 (pt0) REVERT: B 163 ASP cc_start: 0.8066 (p0) cc_final: 0.7745 (p0) REVERT: B 234 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8151 (m-10) REVERT: B 273 ILE cc_start: 0.8665 (mp) cc_final: 0.8433 (mt) REVERT: R 118 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7337 (mt) REVERT: R 131 HIS cc_start: 0.8357 (m-70) cc_final: 0.7765 (m-70) REVERT: R 186 PHE cc_start: 0.7022 (OUTLIER) cc_final: 0.6735 (t80) REVERT: H 18 ARG cc_start: 0.7554 (tpp80) cc_final: 0.7063 (ttm170) REVERT: H 87 ARG cc_start: 0.6594 (mpt180) cc_final: 0.6288 (mtt90) outliers start: 28 outliers final: 22 residues processed: 169 average time/residue: 0.0870 time to fit residues: 20.2801 Evaluate side-chains 169 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 186 PHE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 21 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 9 optimal weight: 0.0020 chunk 71 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 75 GLN R 137 ASN R 175 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.197113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.152643 restraints weight = 9557.032| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.50 r_work: 0.3543 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8074 Z= 0.124 Angle : 0.501 8.659 11025 Z= 0.266 Chirality : 0.043 0.187 1292 Planarity : 0.003 0.062 1423 Dihedral : 3.848 45.555 1188 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.73 % Favored : 97.17 % Rotamer: Outliers : 4.08 % Allowed : 16.20 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 are not related in a simple way. whole: 0.26 (0.26), residues: 1097 helix: 2.21 (0.28), residues: 355 sheet: -1.25 (0.31), residues: 267 loop : -0.46 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 46 TYR 0.020 0.001 TYR A 297 PHE 0.010 0.001 PHE B 235 TRP 0.005 0.001 TRP A 212 HIS 0.002 0.000 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8069) covalent geometry : angle 0.50124 (11015) SS BOND : bond 0.00348 ( 5) SS BOND : angle 0.64736 ( 10) hydrogen bonds : bond 0.03311 ( 393) hydrogen bonds : angle 4.32409 ( 1104) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7659 (tp30) cc_final: 0.7397 (tp30) REVERT: B 59 TYR cc_start: 0.9076 (m-80) cc_final: 0.8817 (m-80) REVERT: B 163 ASP cc_start: 0.8045 (p0) cc_final: 0.7734 (p0) REVERT: B 198 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.7962 (pp) REVERT: B 234 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8187 (m-10) REVERT: B 273 ILE cc_start: 0.8679 (mp) cc_final: 0.8467 (mt) REVERT: R 118 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7307 (mt) REVERT: R 131 HIS cc_start: 0.8311 (m-70) cc_final: 0.7735 (m-70) REVERT: R 186 PHE cc_start: 0.7006 (OUTLIER) cc_final: 0.6713 (t80) REVERT: G 36 ASP cc_start: 0.8784 (t0) cc_final: 0.8578 (t0) REVERT: H 18 ARG cc_start: 0.7446 (tpp80) cc_final: 0.6964 (ttm170) REVERT: H 87 ARG cc_start: 0.6504 (mpt180) cc_final: 0.6239 (mtt90) outliers start: 29 outliers final: 23 residues processed: 166 average time/residue: 0.0831 time to fit residues: 19.0628 Evaluate side-chains 169 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 73 ASP Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 186 PHE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 32 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.192498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.147786 restraints weight = 9670.602| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.56 r_work: 0.3483 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8074 Z= 0.235 Angle : 0.581 7.624 11025 Z= 0.312 Chirality : 0.046 0.189 1292 Planarity : 0.004 0.067 1423 Dihedral : 4.169 46.083 1188 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.38 % Favored : 95.53 % Rotamer: Outliers : 4.51 % Allowed : 15.92 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 are not related in a simple way. whole: 0.07 (0.26), residues: 1097 helix: 2.11 (0.28), residues: 355 sheet: -1.42 (0.30), residues: 285 loop : -0.52 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 216 TYR 0.020 0.002 TYR H 190 PHE 0.020 0.002 PHE H 27 TRP 0.009 0.001 TRP H 36 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00555 ( 8069) covalent geometry : angle 0.58103 (11015) SS BOND : bond 0.00511 ( 5) SS BOND : angle 0.72906 ( 10) hydrogen bonds : bond 0.03714 ( 393) hydrogen bonds : angle 4.53570 ( 1104) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.291 Fit side-chains REVERT: A 208 GLU cc_start: 0.7802 (tp30) cc_final: 0.7550 (tp30) REVERT: B 59 TYR cc_start: 0.9023 (m-80) cc_final: 0.8759 (m-80) REVERT: B 163 ASP cc_start: 0.8162 (p0) cc_final: 0.7876 (p0) REVERT: B 198 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8047 (pp) REVERT: B 234 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.8182 (m-10) REVERT: B 273 ILE cc_start: 0.8662 (mp) cc_final: 0.8438 (mt) REVERT: B 292 PHE cc_start: 0.8698 (m-10) cc_final: 0.8480 (m-80) REVERT: R 131 HIS cc_start: 0.8484 (m-70) cc_final: 0.7927 (m-70) REVERT: R 186 PHE cc_start: 0.7040 (OUTLIER) cc_final: 0.6741 (t80) REVERT: H 18 ARG cc_start: 0.7551 (tpp80) cc_final: 0.7010 (ttm170) REVERT: H 87 ARG cc_start: 0.6692 (mpt180) cc_final: 0.6243 (mtt90) outliers start: 32 outliers final: 24 residues processed: 167 average time/residue: 0.0922 time to fit residues: 20.9593 Evaluate side-chains 170 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 171 ASN Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 186 PHE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 54 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 82 optimal weight: 0.0970 chunk 20 optimal weight: 20.0000 chunk 74 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.0170 chunk 27 optimal weight: 0.6980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.196316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.152278 restraints weight = 9625.490| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.84 r_work: 0.3520 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8074 Z= 0.120 Angle : 0.508 7.754 11025 Z= 0.272 Chirality : 0.043 0.201 1292 Planarity : 0.004 0.065 1423 Dihedral : 3.916 45.681 1188 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.83 % Favored : 97.08 % Rotamer: Outliers : 3.80 % Allowed : 17.18 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 are not related in a simple way. whole: 0.20 (0.26), residues: 1097 helix: 2.18 (0.28), residues: 355 sheet: -1.32 (0.32), residues: 266 loop : -0.48 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 216 TYR 0.023 0.001 TYR A 297 PHE 0.020 0.001 PHE R 105 TRP 0.009 0.001 TRP R 93 HIS 0.002 0.000 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8069) covalent geometry : angle 0.50752 (11015) SS BOND : bond 0.00368 ( 5) SS BOND : angle 0.70383 ( 10) hydrogen bonds : bond 0.03311 ( 393) hydrogen bonds : angle 4.28854 ( 1104) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.301 Fit side-chains REVERT: A 208 GLU cc_start: 0.7689 (tp30) cc_final: 0.7458 (tp30) REVERT: B 59 TYR cc_start: 0.8811 (m-80) cc_final: 0.8585 (m-80) REVERT: B 75 GLN cc_start: 0.8405 (mt0) cc_final: 0.8133 (mt0) REVERT: B 163 ASP cc_start: 0.8069 (p0) cc_final: 0.7764 (p0) REVERT: B 198 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8009 (pp) REVERT: B 234 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.8200 (m-10) REVERT: B 273 ILE cc_start: 0.8692 (mp) cc_final: 0.8461 (mt) REVERT: B 292 PHE cc_start: 0.8603 (m-10) cc_final: 0.8338 (m-10) REVERT: R 131 HIS cc_start: 0.8308 (m-70) cc_final: 0.7757 (m-70) REVERT: R 186 PHE cc_start: 0.6997 (OUTLIER) cc_final: 0.6705 (t80) REVERT: H 18 ARG cc_start: 0.7357 (tpp80) cc_final: 0.6890 (ttm170) REVERT: H 87 ARG cc_start: 0.6564 (mpt180) cc_final: 0.6224 (mtt90) outliers start: 27 outliers final: 24 residues processed: 162 average time/residue: 0.0910 time to fit residues: 20.1342 Evaluate side-chains 168 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 186 PHE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 91 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 25 optimal weight: 0.1980 chunk 86 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.196056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.151571 restraints weight = 9643.420| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.49 r_work: 0.3546 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8074 Z= 0.128 Angle : 0.510 7.853 11025 Z= 0.272 Chirality : 0.043 0.197 1292 Planarity : 0.004 0.063 1423 Dihedral : 3.875 45.831 1188 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.10 % Favored : 96.81 % Rotamer: Outliers : 3.80 % Allowed : 17.46 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 are not related in a simple way. whole: 0.23 (0.27), residues: 1097 helix: 2.26 (0.28), residues: 355 sheet: -1.38 (0.32), residues: 268 loop : -0.45 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 216 TYR 0.021 0.001 TYR A 297 PHE 0.018 0.001 PHE R 105 TRP 0.007 0.001 TRP R 93 HIS 0.002 0.000 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8069) covalent geometry : angle 0.50929 (11015) SS BOND : bond 0.00388 ( 5) SS BOND : angle 0.73020 ( 10) hydrogen bonds : bond 0.03269 ( 393) hydrogen bonds : angle 4.24300 ( 1104) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.287 Fit side-chains REVERT: A 208 GLU cc_start: 0.7724 (tp30) cc_final: 0.7409 (tp30) REVERT: A 295 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8190 (t0) REVERT: B 163 ASP cc_start: 0.8041 (p0) cc_final: 0.7729 (p0) REVERT: B 198 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.7992 (pp) REVERT: B 234 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8192 (m-10) REVERT: B 273 ILE cc_start: 0.8679 (mp) cc_final: 0.8447 (mt) REVERT: B 292 PHE cc_start: 0.8631 (m-10) cc_final: 0.8378 (m-10) REVERT: R 131 HIS cc_start: 0.8283 (m-70) cc_final: 0.7753 (m-70) REVERT: R 186 PHE cc_start: 0.7028 (OUTLIER) cc_final: 0.6721 (t80) REVERT: G 36 ASP cc_start: 0.8776 (t0) cc_final: 0.8564 (t0) REVERT: H 18 ARG cc_start: 0.7274 (tpp80) cc_final: 0.6900 (ttm170) REVERT: H 87 ARG cc_start: 0.6540 (mpt180) cc_final: 0.6203 (mtt90) outliers start: 27 outliers final: 23 residues processed: 157 average time/residue: 0.0869 time to fit residues: 18.6389 Evaluate side-chains 166 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 186 PHE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/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-2.1rc2-6044/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.7166 > 50: distance: 10 - 34: 18.504 distance: 15 - 42: 15.444 distance: 19 - 23: 26.929 distance: 20 - 53: 23.242 distance: 23 - 24: 44.449 distance: 24 - 25: 45.809 distance: 24 - 27: 46.444 distance: 25 - 26: 30.703 distance: 25 - 34: 27.249 distance: 26 - 61: 51.361 distance: 27 - 28: 43.730 distance: 28 - 29: 36.297 distance: 29 - 30: 23.907 distance: 30 - 31: 24.691 distance: 31 - 32: 26.740 distance: 31 - 33: 28.089 distance: 34 - 35: 22.824 distance: 35 - 36: 27.709 distance: 35 - 38: 36.119 distance: 36 - 37: 28.825 distance: 36 - 42: 18.689 distance: 37 - 72: 43.274 distance: 38 - 39: 13.753 distance: 38 - 40: 56.339 distance: 39 - 41: 35.639 distance: 42 - 43: 14.706 distance: 43 - 44: 34.310 distance: 43 - 46: 24.041 distance: 44 - 45: 31.186 distance: 44 - 53: 19.708 distance: 45 - 77: 33.558 distance: 46 - 47: 10.832 distance: 47 - 48: 23.856 distance: 47 - 49: 22.272 distance: 48 - 50: 18.579 distance: 49 - 51: 21.471 distance: 50 - 52: 6.357 distance: 51 - 52: 7.572 distance: 53 - 54: 38.538 distance: 54 - 55: 32.951 distance: 54 - 57: 28.044 distance: 55 - 56: 39.723 distance: 55 - 61: 34.685 distance: 56 - 85: 52.522 distance: 57 - 58: 20.413 distance: 58 - 59: 44.579 distance: 58 - 60: 27.935 distance: 61 - 62: 31.941 distance: 62 - 63: 10.678 distance: 62 - 65: 16.295 distance: 63 - 64: 33.619 distance: 63 - 72: 13.283 distance: 64 - 90: 36.565 distance: 65 - 66: 21.000 distance: 66 - 67: 15.209 distance: 66 - 68: 18.871 distance: 67 - 69: 8.422 distance: 68 - 70: 6.465 distance: 69 - 71: 6.181 distance: 70 - 71: 7.682 distance: 72 - 73: 59.781 distance: 73 - 74: 32.675 distance: 73 - 76: 47.920 distance: 74 - 75: 62.717 distance: 74 - 77: 18.975 distance: 75 - 95: 45.492 distance: 77 - 78: 15.444 distance: 78 - 79: 21.476 distance: 78 - 81: 45.629 distance: 79 - 80: 8.162 distance: 79 - 85: 37.813 distance: 80 - 100: 27.966 distance: 81 - 82: 32.066 distance: 82 - 83: 12.250 distance: 82 - 84: 10.485 distance: 85 - 86: 26.714 distance: 86 - 87: 29.952 distance: 86 - 89: 20.609 distance: 87 - 88: 46.632 distance: 87 - 90: 55.867 distance: 88 - 108: 28.127 distance: 90 - 91: 44.292 distance: 91 - 92: 12.806 distance: 91 - 94: 9.775 distance: 92 - 93: 44.457 distance: 92 - 95: 21.250 distance: 93 - 113: 31.408 distance: 95 - 96: 35.591 distance: 96 - 97: 11.824 distance: 96 - 99: 34.140 distance: 97 - 98: 22.750 distance: 97 - 100: 17.179 distance: 98 - 120: 11.817