Starting phenix.real_space_refine on Sun May 3 01:54:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jsr_36627/05_2026/8jsr_36627.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jsr_36627/05_2026/8jsr_36627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jsr_36627/05_2026/8jsr_36627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jsr_36627/05_2026/8jsr_36627.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jsr_36627/05_2026/8jsr_36627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jsr_36627/05_2026/8jsr_36627.map" } resolution = 2.9 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= 1.000 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 65 5.16 5 C 6371 2.51 5 N 1717 2.21 5 O 1848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 10001 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2209 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 11, 'TRANS': 270} Chain breaks: 2 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'TRP:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "A" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1974 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 1 Chain: "B" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2610 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'UYI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.33, per 1000 atoms: 0.23 Number of scatterers: 10001 At special positions: 0 Unit cell: (90.64, 122.32, 133.76, 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 65 16.00 O 1848 8.00 N 1717 7.00 C 6371 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 116 " - pdb=" SG CYS R 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 342.9 milliseconds 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2380 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 15 sheets defined 37.0% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'R' and resid 39 through 71 Processing helix chain 'R' and resid 76 through 95 removed outlier: 3.506A pdb=" N LEU R 80 " --> pdb=" O THR R 76 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 105 removed outlier: 3.763A pdb=" N ASP R 99 " --> pdb=" O CYS R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 147 removed outlier: 3.840A pdb=" N GLN R 120 " --> pdb=" O CYS R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 155 Processing helix chain 'R' and resid 156 through 175 removed outlier: 3.610A pdb=" N LEU R 162 " --> pdb=" O GLY R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 181 removed outlier: 3.662A pdb=" N LEU R 181 " --> pdb=" O PRO R 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 177 through 181' Processing helix chain 'R' and resid 201 through 208 Processing helix chain 'R' and resid 208 through 241 removed outlier: 3.768A pdb=" N VAL R 212 " --> pdb=" O GLY R 208 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE R 220 " --> pdb=" O VAL R 216 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE R 221 " --> pdb=" O SER R 217 " (cutoff:3.500A) Proline residue: R 224 - end of helix removed outlier: 3.604A pdb=" N ARG R 241 " --> pdb=" O ARG R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 289 removed outlier: 3.674A pdb=" N VAL R 262 " --> pdb=" O HIS R 258 " (cutoff:3.500A) Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 296 through 325 removed outlier: 4.186A pdb=" N ILE R 300 " --> pdb=" O GLU R 296 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA R 316 " --> pdb=" O PHE R 312 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA R 317 " --> pdb=" O TYR R 313 " (cutoff:3.500A) Proline residue: R 320 - end of helix Processing helix chain 'R' and resid 329 through 338 Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.702A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.591A pdb=" N GLN A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.564A pdb=" N GLY A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 removed outlier: 3.709A pdb=" N ASP A 277 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.851A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 319 removed outlier: 3.749A pdb=" N PHE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.543A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.855A pdb=" N LYS C 65 " --> pdb=" O ASP C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.707A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 224 removed outlier: 3.741A pdb=" N VAL C 224 " --> pdb=" O ALA C 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.787A 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 'N' and resid 28 through 32 removed outlier: 3.589A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.832A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 182 through 186 Processing sheet with id=AA2, first strand: chain 'A' and resid 184 through 190 removed outlier: 4.712A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.776A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.193A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.807A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.601A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.727A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.363A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.622A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.817A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'C' and resid 146 through 148 removed outlier: 5.974A pdb=" N VAL C 147 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU C 174 " --> pdb=" O TYR C 190 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TYR C 190 " --> pdb=" O LEU C 174 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP C 176 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.546A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 10 through 11 removed outlier: 5.965A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1368 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: 1.86 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3224 1.35 - 1.47: 2561 1.47 - 1.59: 4332 1.59 - 1.71: 4 1.71 - 1.83: 92 Bond restraints: 10213 Sorted by residual: bond pdb=" C07 UYI R 601 " pdb=" C18 UYI R 601 " ideal model delta sigma weight residual 1.550 1.661 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C33 UYI R 601 " pdb=" N35 UYI R 601 " ideal model delta sigma weight residual 1.393 1.471 -0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" C07 UYI R 601 " pdb=" C08 UYI R 601 " ideal model delta sigma weight residual 1.548 1.604 -0.056 2.00e-02 2.50e+03 7.86e+00 bond pdb=" C24 UYI R 601 " pdb=" C25 UYI R 601 " ideal model delta sigma weight residual 1.561 1.615 -0.054 2.00e-02 2.50e+03 7.37e+00 bond pdb=" C26 UYI R 601 " pdb=" C27 UYI R 601 " ideal model delta sigma weight residual 1.504 1.555 -0.051 2.00e-02 2.50e+03 6.44e+00 ... (remaining 10208 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 13628 1.97 - 3.94: 177 3.94 - 5.92: 24 5.92 - 7.89: 11 7.89 - 9.86: 3 Bond angle restraints: 13843 Sorted by residual: angle pdb=" C ARG C 191 " pdb=" N MET C 192 " pdb=" CA MET C 192 " ideal model delta sigma weight residual 121.54 128.64 -7.10 1.91e+00 2.74e-01 1.38e+01 angle pdb=" C24 UYI R 601 " pdb=" C25 UYI R 601 " pdb=" N20 UYI R 601 " ideal model delta sigma weight residual 113.13 122.99 -9.86 3.00e+00 1.11e-01 1.08e+01 angle pdb=" N ALA R 298 " pdb=" CA ALA R 298 " pdb=" C ALA R 298 " ideal model delta sigma weight residual 111.07 114.49 -3.42 1.07e+00 8.73e-01 1.02e+01 angle pdb=" C07 UYI R 601 " pdb=" C18 UYI R 601 " pdb=" N20 UYI R 601 " ideal model delta sigma weight residual 119.41 128.39 -8.98 3.00e+00 1.11e-01 8.97e+00 angle pdb=" CA CYS R 198 " pdb=" CB CYS R 198 " pdb=" SG CYS R 198 " ideal model delta sigma weight residual 114.40 120.93 -6.53 2.30e+00 1.89e-01 8.07e+00 ... (remaining 13838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.00: 5660 22.00 - 44.00: 372 44.00 - 65.99: 40 65.99 - 87.99: 9 87.99 - 109.99: 2 Dihedral angle restraints: 6083 sinusoidal: 2390 harmonic: 3693 Sorted by residual: dihedral pdb=" CA SER C 53 " pdb=" C SER C 53 " pdb=" N GLY C 54 " pdb=" CA GLY C 54 " ideal model delta harmonic sigma weight residual 180.00 157.21 22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -122.53 36.53 1 1.00e+01 1.00e-02 1.89e+01 dihedral pdb=" CA CYS B 204 " pdb=" C CYS B 204 " pdb=" N ASP B 205 " pdb=" CA ASP B 205 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 6080 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1408 0.070 - 0.140: 154 0.140 - 0.210: 1 0.210 - 0.280: 0 0.280 - 0.350: 1 Chirality restraints: 1564 Sorted by residual: chirality pdb=" C07 UYI R 601 " pdb=" C08 UYI R 601 " pdb=" C18 UYI R 601 " pdb=" N06 UYI R 601 " both_signs ideal model delta sigma weight residual False 2.71 2.36 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA THR B 223 " pdb=" N THR B 223 " pdb=" C THR B 223 " pdb=" CB THR B 223 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA CYS R 198 " pdb=" N CYS R 198 " pdb=" C CYS R 198 " pdb=" CB CYS R 198 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 1561 not shown) Planarity restraints: 1752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 279 " -0.014 2.00e-02 2.50e+03 2.70e-02 7.28e+00 pdb=" C PHE R 279 " 0.047 2.00e-02 2.50e+03 pdb=" O PHE R 279 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS R 280 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 301 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.96e+00 pdb=" C SER R 301 " 0.046 2.00e-02 2.50e+03 pdb=" O SER R 301 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN R 302 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY R 176 " 0.043 5.00e-02 4.00e+02 6.47e-02 6.69e+00 pdb=" N PRO R 177 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO R 177 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 177 " 0.036 5.00e-02 4.00e+02 ... (remaining 1749 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 458 2.72 - 3.27: 9453 3.27 - 3.81: 16054 3.81 - 4.36: 20469 4.36 - 4.90: 35901 Nonbonded interactions: 82335 Sorted by model distance: nonbonded pdb=" O GLY C 8 " pdb=" OG1 THR C 115 " model vdw 2.178 3.040 nonbonded pdb=" NH1 ARG A 205 " pdb=" OD1 ASP B 186 " model vdw 2.220 3.120 nonbonded pdb=" OD1 ASP R 99 " pdb=" NH2 ARG R 102 " model vdw 2.239 3.120 nonbonded pdb=" O TYR A 285 " pdb=" NH1 ARG A 303 " model vdw 2.248 3.120 nonbonded pdb=" OG SER C 52 " pdb=" O GLY C 54 " model vdw 2.249 3.040 ... (remaining 82330 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: 3.320 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.090 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 0.111 10217 Z= 0.170 Angle : 0.600 9.859 13851 Z= 0.312 Chirality : 0.042 0.350 1564 Planarity : 0.004 0.065 1752 Dihedral : 14.434 109.988 3691 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.37 % Allowed : 7.20 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.82 (0.23), residues: 1255 helix: 1.74 (0.25), residues: 411 sheet: 0.49 (0.28), residues: 340 loop : -0.36 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 241 TYR 0.012 0.001 TYR R 313 PHE 0.015 0.001 PHE B 234 TRP 0.011 0.001 TRP A 211 HIS 0.006 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00364 (10213) covalent geometry : angle 0.59891 (13843) SS BOND : bond 0.00448 ( 4) SS BOND : angle 1.53164 ( 8) hydrogen bonds : bond 0.17271 ( 488) hydrogen bonds : angle 6.62250 ( 1368) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 161 time to evaluate : 0.329 Fit side-chains REVERT: A 266 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7420 (mm-30) REVERT: B 46 ARG cc_start: 0.8003 (mpt90) cc_final: 0.7801 (mtm-85) REVERT: B 186 ASP cc_start: 0.8331 (m-30) cc_final: 0.8106 (m-30) REVERT: N 31 ASN cc_start: 0.8686 (m110) cc_final: 0.8152 (m110) outliers start: 4 outliers final: 0 residues processed: 163 average time/residue: 0.7471 time to fit residues: 128.7428 Evaluate side-chains 118 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.0980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 324 ASN A 213 GLN A 261 GLN A 338 ASN A 359 ASN B 6 GLN B 110 ASN B 155 ASN B 183 HIS B 268 ASN C 171 ASN N 31 ASN N 74 ASN N 84 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.176429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.140388 restraints weight = 11114.088| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.59 r_work: 0.3468 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10217 Z= 0.127 Angle : 0.545 9.023 13851 Z= 0.289 Chirality : 0.041 0.136 1564 Planarity : 0.004 0.065 1752 Dihedral : 7.497 100.790 1432 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.66 % Allowed : 14.39 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.01 (0.23), residues: 1255 helix: 2.05 (0.25), residues: 416 sheet: 0.56 (0.27), residues: 339 loop : -0.39 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 284 TYR 0.014 0.001 TYR R 313 PHE 0.020 0.001 PHE R 54 TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00280 (10213) covalent geometry : angle 0.54433 (13843) SS BOND : bond 0.00351 ( 4) SS BOND : angle 1.20935 ( 8) hydrogen bonds : bond 0.04450 ( 488) hydrogen bonds : angle 4.63822 ( 1368) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.373 Fit side-chains REVERT: R 43 LEU cc_start: 0.6712 (OUTLIER) cc_final: 0.5993 (tt) REVERT: R 131 VAL cc_start: 0.7615 (m) cc_final: 0.6802 (p) REVERT: A 266 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7072 (mm-30) REVERT: A 345 ASP cc_start: 0.8549 (m-30) cc_final: 0.8234 (m-30) REVERT: B 135 VAL cc_start: 0.9153 (p) cc_final: 0.8931 (t) REVERT: C 43 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8162 (mtpm) REVERT: C 140 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8759 (mmm) REVERT: N 31 ASN cc_start: 0.8516 (m-40) cc_final: 0.8274 (m110) outliers start: 18 outliers final: 6 residues processed: 142 average time/residue: 0.7650 time to fit residues: 114.9198 Evaluate side-chains 137 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 140 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 18 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 76 optimal weight: 0.0670 chunk 125 optimal weight: 1.9990 chunk 15 optimal weight: 40.0000 chunk 39 optimal weight: 2.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 ASN R 305 ASN A 28 GLN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.176329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.138674 restraints weight = 11078.967| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.54 r_work: 0.3473 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10217 Z= 0.125 Angle : 0.523 7.702 13851 Z= 0.277 Chirality : 0.041 0.136 1564 Planarity : 0.004 0.061 1752 Dihedral : 7.305 104.348 1432 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.58 % Allowed : 16.33 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.11 (0.23), residues: 1255 helix: 2.22 (0.25), residues: 417 sheet: 0.57 (0.27), residues: 345 loop : -0.39 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 284 TYR 0.012 0.001 TYR C 190 PHE 0.014 0.001 PHE B 234 TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00282 (10213) covalent geometry : angle 0.52235 (13843) SS BOND : bond 0.00349 ( 4) SS BOND : angle 1.10777 ( 8) hydrogen bonds : bond 0.04167 ( 488) hydrogen bonds : angle 4.39253 ( 1368) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.388 Fit side-chains REVERT: R 103 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6740 (pt) REVERT: R 131 VAL cc_start: 0.7650 (m) cc_final: 0.6785 (p) REVERT: A 28 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7696 (mp-120) REVERT: A 266 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7118 (mm-30) REVERT: A 345 ASP cc_start: 0.8582 (m-30) cc_final: 0.8303 (m-30) REVERT: B 59 TYR cc_start: 0.9074 (OUTLIER) cc_final: 0.8127 (m-80) REVERT: B 153 ASP cc_start: 0.8161 (m-30) cc_final: 0.7875 (p0) REVERT: B 197 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7685 (mtp180) REVERT: C 43 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8167 (mtpm) REVERT: N 31 ASN cc_start: 0.8451 (m-40) cc_final: 0.8238 (m110) outliers start: 28 outliers final: 12 residues processed: 145 average time/residue: 0.7563 time to fit residues: 116.0995 Evaluate side-chains 138 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 103 LEU Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 213 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 111 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 52 GLN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.176105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.138519 restraints weight = 11187.066| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.55 r_work: 0.3483 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10217 Z= 0.128 Angle : 0.520 7.503 13851 Z= 0.275 Chirality : 0.041 0.133 1564 Planarity : 0.004 0.054 1752 Dihedral : 7.207 104.598 1432 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.14 % Allowed : 17.25 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.14 (0.23), residues: 1255 helix: 2.29 (0.25), residues: 417 sheet: 0.59 (0.27), residues: 345 loop : -0.43 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 284 TYR 0.012 0.001 TYR C 190 PHE 0.015 0.001 PHE B 234 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00291 (10213) covalent geometry : angle 0.51981 (13843) SS BOND : bond 0.00356 ( 4) SS BOND : angle 1.02950 ( 8) hydrogen bonds : bond 0.04082 ( 488) hydrogen bonds : angle 4.33748 ( 1368) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.387 Fit side-chains REVERT: R 43 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6038 (tt) REVERT: R 103 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6604 (pt) REVERT: R 131 VAL cc_start: 0.7531 (m) cc_final: 0.6679 (p) REVERT: A 266 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7063 (mm-30) REVERT: A 345 ASP cc_start: 0.8571 (m-30) cc_final: 0.8256 (m-30) REVERT: B 59 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.8096 (m-80) REVERT: B 153 ASP cc_start: 0.8168 (m-30) cc_final: 0.7900 (p0) REVERT: B 197 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7477 (mtp180) REVERT: C 19 LYS cc_start: 0.8657 (tttp) cc_final: 0.8447 (tttt) REVERT: C 43 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8144 (mtpm) REVERT: C 113 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7468 (mp10) outliers start: 34 outliers final: 15 residues processed: 142 average time/residue: 0.6859 time to fit residues: 103.5000 Evaluate side-chains 141 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 103 LEU Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 213 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 76 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 27 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 24 optimal weight: 0.0770 chunk 87 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 324 ASN A 28 GLN A 52 GLN B 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.175822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.139043 restraints weight = 11131.136| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.48 r_work: 0.3498 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10217 Z= 0.116 Angle : 0.502 7.247 13851 Z= 0.266 Chirality : 0.040 0.132 1564 Planarity : 0.004 0.049 1752 Dihedral : 6.989 105.750 1432 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.32 % Allowed : 17.99 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.20 (0.23), residues: 1255 helix: 2.35 (0.25), residues: 417 sheet: 0.63 (0.27), residues: 345 loop : -0.42 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 284 TYR 0.012 0.001 TYR C 190 PHE 0.022 0.001 PHE R 54 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00260 (10213) covalent geometry : angle 0.50115 (13843) SS BOND : bond 0.00332 ( 4) SS BOND : angle 0.98898 ( 8) hydrogen bonds : bond 0.03855 ( 488) hydrogen bonds : angle 4.21680 ( 1368) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: R 43 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6093 (tt) REVERT: R 103 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6548 (pt) REVERT: R 131 VAL cc_start: 0.7535 (m) cc_final: 0.6663 (p) REVERT: A 28 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7869 (mp-120) REVERT: A 266 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7092 (mm-30) REVERT: A 276 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7343 (pm20) REVERT: A 345 ASP cc_start: 0.8556 (m-30) cc_final: 0.8236 (m-30) REVERT: B 59 TYR cc_start: 0.9079 (OUTLIER) cc_final: 0.8173 (m-80) REVERT: B 153 ASP cc_start: 0.8124 (m-30) cc_final: 0.7904 (p0) REVERT: B 197 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7420 (mtp180) REVERT: C 19 LYS cc_start: 0.8638 (tttp) cc_final: 0.8431 (tttt) REVERT: C 43 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8138 (mtpm) REVERT: C 113 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7464 (mp10) outliers start: 36 outliers final: 20 residues processed: 141 average time/residue: 0.6732 time to fit residues: 101.0361 Evaluate side-chains 148 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 103 LEU Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 102 optimal weight: 0.0970 chunk 107 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 120 optimal weight: 0.0040 chunk 39 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 49 optimal weight: 0.4980 chunk 54 optimal weight: 4.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 324 ASN A 28 GLN A 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.175426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.138689 restraints weight = 11190.531| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.50 r_work: 0.3480 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10217 Z= 0.121 Angle : 0.511 7.126 13851 Z= 0.270 Chirality : 0.040 0.131 1564 Planarity : 0.004 0.045 1752 Dihedral : 6.948 106.300 1432 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.32 % Allowed : 19.46 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.18 (0.23), residues: 1255 helix: 2.36 (0.25), residues: 417 sheet: 0.61 (0.27), residues: 345 loop : -0.44 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 284 TYR 0.012 0.001 TYR C 190 PHE 0.018 0.001 PHE R 54 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00274 (10213) covalent geometry : angle 0.51050 (13843) SS BOND : bond 0.00399 ( 4) SS BOND : angle 1.01318 ( 8) hydrogen bonds : bond 0.03884 ( 488) hydrogen bonds : angle 4.21896 ( 1368) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: R 43 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6101 (tt) REVERT: R 65 MET cc_start: 0.6446 (OUTLIER) cc_final: 0.6136 (mtm) REVERT: R 103 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6573 (pt) REVERT: R 131 VAL cc_start: 0.7571 (m) cc_final: 0.6682 (p) REVERT: A 266 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7104 (mm-30) REVERT: A 276 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7330 (pm20) REVERT: A 345 ASP cc_start: 0.8576 (m-30) cc_final: 0.8292 (m-30) REVERT: B 59 TYR cc_start: 0.9060 (OUTLIER) cc_final: 0.8147 (m-80) REVERT: B 134 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8192 (ptt180) REVERT: B 153 ASP cc_start: 0.8183 (m-30) cc_final: 0.7957 (p0) REVERT: B 197 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7453 (mtp180) REVERT: C 19 LYS cc_start: 0.8657 (tttp) cc_final: 0.8454 (tttt) REVERT: C 43 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8143 (mtpm) outliers start: 36 outliers final: 22 residues processed: 139 average time/residue: 0.6767 time to fit residues: 100.0438 Evaluate side-chains 148 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 65 MET Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 103 LEU Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 3 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 119 optimal weight: 0.3980 chunk 122 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 59 optimal weight: 0.1980 chunk 51 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 324 ASN A 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.175877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.139255 restraints weight = 11105.226| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.49 r_work: 0.3493 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10217 Z= 0.114 Angle : 0.499 6.909 13851 Z= 0.264 Chirality : 0.040 0.131 1564 Planarity : 0.004 0.041 1752 Dihedral : 6.819 107.061 1432 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.23 % Allowed : 19.74 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.22 (0.23), residues: 1255 helix: 2.42 (0.25), residues: 417 sheet: 0.60 (0.27), residues: 345 loop : -0.41 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 160 TYR 0.012 0.001 TYR R 313 PHE 0.017 0.001 PHE R 54 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00255 (10213) covalent geometry : angle 0.49831 (13843) SS BOND : bond 0.00379 ( 4) SS BOND : angle 0.97402 ( 8) hydrogen bonds : bond 0.03770 ( 488) hydrogen bonds : angle 4.16428 ( 1368) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: R 103 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6520 (pt) REVERT: R 131 VAL cc_start: 0.7527 (m) cc_final: 0.6631 (p) REVERT: A 266 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7046 (mm-30) REVERT: A 276 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7309 (pm20) REVERT: A 345 ASP cc_start: 0.8567 (m-30) cc_final: 0.8258 (m-30) REVERT: B 59 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.8149 (m-80) REVERT: B 134 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8194 (ptt180) REVERT: B 153 ASP cc_start: 0.8168 (m-30) cc_final: 0.7957 (p0) REVERT: B 197 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7422 (mtp180) REVERT: B 217 MET cc_start: 0.8285 (pmm) cc_final: 0.8039 (ppp) REVERT: C 19 LYS cc_start: 0.8649 (tttp) cc_final: 0.8448 (tttt) REVERT: C 43 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8110 (mtpm) outliers start: 35 outliers final: 23 residues processed: 144 average time/residue: 0.6502 time to fit residues: 99.7180 Evaluate side-chains 148 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 103 LEU Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 112 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 324 ASN A 28 GLN A 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.174243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.136654 restraints weight = 11160.460| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.52 r_work: 0.3452 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10217 Z= 0.148 Angle : 0.546 7.616 13851 Z= 0.288 Chirality : 0.041 0.136 1564 Planarity : 0.004 0.043 1752 Dihedral : 7.002 106.893 1432 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.23 % Allowed : 19.93 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.12 (0.23), residues: 1255 helix: 2.31 (0.25), residues: 417 sheet: 0.56 (0.27), residues: 349 loop : -0.46 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 160 TYR 0.013 0.001 TYR R 313 PHE 0.016 0.001 PHE R 54 TRP 0.015 0.002 TRP B 82 HIS 0.006 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00346 (10213) covalent geometry : angle 0.54515 (13843) SS BOND : bond 0.00425 ( 4) SS BOND : angle 1.05168 ( 8) hydrogen bonds : bond 0.04217 ( 488) hydrogen bonds : angle 4.33197 ( 1368) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: R 43 LEU cc_start: 0.6947 (mm) cc_final: 0.5952 (tt) REVERT: A 28 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7884 (mp-120) REVERT: A 266 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7097 (mm-30) REVERT: A 276 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7370 (pm20) REVERT: A 345 ASP cc_start: 0.8640 (m-30) cc_final: 0.8343 (m-30) REVERT: B 59 TYR cc_start: 0.9062 (OUTLIER) cc_final: 0.8171 (m-80) REVERT: B 134 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8221 (ptt180) REVERT: B 153 ASP cc_start: 0.8218 (m-30) cc_final: 0.7916 (p0) REVERT: B 197 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7464 (mtp180) REVERT: B 215 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7793 (mm-30) REVERT: C 19 LYS cc_start: 0.8666 (tttp) cc_final: 0.8464 (tttt) outliers start: 35 outliers final: 21 residues processed: 140 average time/residue: 0.6496 time to fit residues: 97.0321 Evaluate side-chains 145 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 chunk 78 optimal weight: 0.1980 chunk 90 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 324 ASN A 28 GLN A 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.176512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.139310 restraints weight = 11145.798| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.53 r_work: 0.3486 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10217 Z= 0.111 Angle : 0.501 7.226 13851 Z= 0.265 Chirality : 0.040 0.136 1564 Planarity : 0.004 0.039 1752 Dihedral : 6.782 108.139 1432 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.68 % Allowed : 20.39 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.19 (0.23), residues: 1255 helix: 2.40 (0.25), residues: 417 sheet: 0.59 (0.27), residues: 344 loop : -0.45 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 160 TYR 0.013 0.001 TYR C 190 PHE 0.017 0.001 PHE R 54 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00245 (10213) covalent geometry : angle 0.50051 (13843) SS BOND : bond 0.00345 ( 4) SS BOND : angle 0.90773 ( 8) hydrogen bonds : bond 0.03758 ( 488) hydrogen bonds : angle 4.19702 ( 1368) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: R 43 LEU cc_start: 0.6987 (mm) cc_final: 0.6005 (tt) REVERT: R 131 VAL cc_start: 0.7595 (m) cc_final: 0.6694 (p) REVERT: A 266 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7109 (mm-30) REVERT: A 276 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7368 (pm20) REVERT: A 345 ASP cc_start: 0.8567 (m-30) cc_final: 0.8265 (m-30) REVERT: B 59 TYR cc_start: 0.9073 (OUTLIER) cc_final: 0.8177 (m-80) REVERT: B 134 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8213 (ptt180) REVERT: B 153 ASP cc_start: 0.8184 (m-30) cc_final: 0.7944 (p0) REVERT: B 197 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7398 (mtp180) REVERT: B 215 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7737 (mm-30) REVERT: B 217 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.8017 (ppp) REVERT: C 19 LYS cc_start: 0.8657 (tttp) cc_final: 0.8453 (tttt) outliers start: 29 outliers final: 20 residues processed: 134 average time/residue: 0.6835 time to fit residues: 97.5217 Evaluate side-chains 144 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 99 CYS 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: 55.188 > 50: distance: 51 - 56: 8.101 distance: 56 - 57: 4.686 distance: 56 - 193: 4.753 distance: 57 - 58: 4.798 distance: 57 - 60: 8.936 distance: 58 - 59: 3.630 distance: 59 - 190: 3.590 distance: 60 - 61: 3.850 distance: 61 - 63: 4.215 distance: 62 - 64: 5.408 distance: 64 - 66: 8.607 distance: 65 - 66: 8.214 distance: 67 - 68: 3.832 distance: 67 - 131: 8.329 distance: 68 - 69: 5.938 distance: 68 - 71: 5.964 distance: 69 - 75: 6.207 distance: 70 - 128: 8.749 distance: 71 - 72: 8.788 distance: 72 - 73: 9.261 distance: 72 - 74: 13.607 distance: 75 - 76: 4.821 distance: 75 - 175: 5.860 distance: 76 - 77: 4.336 distance: 77 - 78: 10.531 distance: 78 - 172: 15.373 distance: 79 - 80: 8.277 distance: 80 - 81: 7.221 distance: 81 - 82: 8.266 distance: 81 - 83: 7.608 distance: 85 - 86: 7.170 distance: 85 - 88: 3.227 distance: 86 - 87: 5.318 distance: 86 - 95: 4.399 distance: 89 - 90: 12.029 distance: 90 - 91: 3.695 distance: 92 - 93: 6.951 distance: 92 - 94: 3.251 distance: 95 - 96: 5.208 distance: 95 - 101: 18.392 distance: 96 - 97: 17.275 distance: 96 - 99: 18.036 distance: 97 - 98: 33.480 distance: 97 - 102: 9.421 distance: 99 - 100: 13.065 distance: 100 - 101: 6.467 distance: 102 - 103: 7.592 distance: 103 - 104: 29.830 distance: 104 - 105: 26.523 distance: 104 - 106: 22.011 distance: 106 - 107: 7.954 distance: 107 - 108: 4.396 distance: 107 - 110: 4.343 distance: 108 - 109: 9.021 distance: 108 - 115: 7.859 distance: 110 - 111: 5.432 distance: 111 - 112: 7.785 distance: 112 - 113: 8.944 distance: 112 - 114: 3.778 distance: 115 - 116: 3.190 distance: 116 - 119: 4.142 distance: 117 - 121: 3.712 distance: 121 - 127: 3.695 distance: 122 - 123: 6.922 distance: 122 - 125: 4.666 distance: 123 - 124: 16.137 distance: 125 - 126: 6.495 distance: 126 - 127: 5.096 distance: 129 - 130: 4.180 distance: 129 - 132: 7.388 distance: 130 - 131: 4.066 distance: 130 - 137: 3.057 distance: 132 - 133: 3.278 distance: 133 - 134: 6.051 distance: 134 - 135: 4.557 distance: 134 - 136: 4.527