Starting phenix.real_space_refine on Fri Jul 3 18:22:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7qne_14076/07_2026/7qne_14076.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qne_14076/07_2026/7qne_14076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7qne_14076/07_2026/7qne_14076.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7qne_14076/07_2026/7qne_14076.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qne_14076/07_2026/7qne_14076.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qne_14076/07_2026/7qne_14076.map" model { file = "/net/cci-nas-00/data/ceres_data/7qne_14076/07_2026/7qne_14076.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qne_14076/07_2026/7qne_14076.cif" } resolution = 2.7 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 82 5.16 5 Cl 3 4.86 5 C 9908 2.51 5 N 2482 2.21 5 O 2821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15302 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2801 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 345, 2793 Classifications: {'peptide': 345} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 330} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 345, 2793 Classifications: {'peptide': 345} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 330} Chain breaks: 1 bond proxies already assigned to first conformer: 2855 Chain: "B" Number of atoms: 2751 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2742 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 334, 2742 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain breaks: 1 bond proxies already assigned to first conformer: 2804 Chain: "C" Number of atoms: 2712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2712 Classifications: {'peptide': 329} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 315} Chain breaks: 1 Chain: "D" Number of atoms: 2795 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 343, 2780 Classifications: {'peptide': 343} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 328} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 343, 2780 Classifications: {'peptide': 343} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 328} Chain breaks: 1 bond proxies already assigned to first conformer: 2833 Chain: "E" Number of atoms: 2745 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2740 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 334, 2740 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain breaks: 1 bond proxies already assigned to first conformer: 2807 Chain: "G" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 949 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "a" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 66 Unusual residues: {' CL': 1, 'D10': 1, 'OCT': 1, 'PIO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'D10': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' CL': 1, 'D10': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Unusual residues: {' CL': 1, 'EIE': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'D10': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.99, per 1000 atoms: 0.33 Number of scatterers: 15302 At special positions: 0 Unit cell: (103.936, 102.144, 136.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 3 17.00 S 82 16.00 P 6 15.00 O 2821 8.00 N 2482 7.00 C 9908 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " 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 Links applied ALPHA1-2 " MAN a 4 " - " MAN a 5 " " MAN a 5 " - " MAN a 6 " ALPHA1-3 " BMA F 3 " - " MAN F 6 " " MAN F 4 " - " MAN F 5 " " BMA H 3 " - " MAN H 6 " " MAN H 4 " - " MAN H 5 " " BMA a 3 " - " MAN a 4 " " MAN a 7 " - " MAN a 8 " " BMA d 3 " - " MAN d 4 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " " BMA a 3 " - " MAN a 7 " " MAN a 7 " - " MAN a 9 " " BMA d 3 " - " MAN d 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG C 503 " - " ASN C 208 " " NAG F 1 " - " ASN B 149 " " NAG H 1 " - " ASN E 149 " " NAG a 1 " - " ASN A 111 " " NAG b 1 " - " ASN B 80 " " NAG d 1 " - " ASN D 111 " " NAG e 1 " - " ASN E 80 " Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 867.4 milliseconds 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 17 sheets defined 38.2% alpha, 41.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 removed outlier: 3.906A pdb=" N LEU A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 76 removed outlier: 3.532A pdb=" N LYS A 76 " --> pdb=" O GLU A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 73 through 76' Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 142 through 146 removed outlier: 4.379A pdb=" N ASP A 145 " --> pdb=" O HIS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.768A pdb=" N SER A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 251 through 275 removed outlier: 3.501A pdb=" N ASN A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 310 removed outlier: 3.614A pdb=" N PHE A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 418 removed outlier: 3.944A pdb=" N ILE A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Proline residue: A 401 - end of helix Processing helix chain 'B' and resid 11 through 21 Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 91 removed outlier: 3.550A pdb=" N LEU B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 218 through 225 removed outlier: 3.691A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 242 removed outlier: 3.521A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 272 removed outlier: 3.582A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 308 removed outlier: 3.741A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 447 removed outlier: 3.549A pdb=" N ASP B 424 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 85 through 88 Processing helix chain 'C' and resid 99 through 103 removed outlier: 3.979A pdb=" N MET C 102 " --> pdb=" O ASN C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 240 removed outlier: 3.524A pdb=" N ILE C 238 " --> pdb=" O GLY C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 252 Processing helix chain 'C' and resid 252 through 257 removed outlier: 4.051A pdb=" N TRP C 256 " --> pdb=" O TRP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 284 removed outlier: 3.516A pdb=" N THR C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ARG C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 322 Processing helix chain 'C' and resid 406 through 408 No H-bonds generated for 'chain 'C' and resid 406 through 408' Processing helix chain 'C' and resid 409 through 435 removed outlier: 3.811A pdb=" N ILE C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 73 through 76 Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 142 through 146 removed outlier: 4.392A pdb=" N ASP D 145 " --> pdb=" O HIS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 223 through 230 removed outlier: 3.511A pdb=" N ILE D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.883A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 247 No H-bonds generated for 'chain 'D' and resid 245 through 247' Processing helix chain 'D' and resid 251 through 277 removed outlier: 3.564A pdb=" N THR D 262 " --> pdb=" O PHE D 258 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 309 removed outlier: 3.591A pdb=" N LEU D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 416 removed outlier: 3.688A pdb=" N ILE D 398 " --> pdb=" O ARG D 394 " (cutoff:3.500A) Proline residue: D 401 - end of helix Processing helix chain 'E' and resid 9 through 21 Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 84 through 91 Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 218 through 225 removed outlier: 3.560A pdb=" N LEU E 223 " --> pdb=" O GLY E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 237 removed outlier: 3.740A pdb=" N SER E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TRP E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 242 Processing helix chain 'E' and resid 246 through 272 removed outlier: 3.544A pdb=" N GLU E 270 " --> pdb=" O THR E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 308 removed outlier: 3.549A pdb=" N ALA E 300 " --> pdb=" O LEU E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 447 removed outlier: 3.781A pdb=" N ILE E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Proline residue: E 432 - end of helix Processing helix chain 'G' and resid 86 through 90 Processing helix chain 'G' and resid 106 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 109 removed outlier: 7.063A pdb=" N GLU A 59 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR A 61 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N PHE A 50 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASP A 63 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS A 71 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU A 40 " --> pdb=" O LYS A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 117 through 121 removed outlier: 7.063A pdb=" N GLU A 59 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR A 61 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N PHE A 50 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASP A 63 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS A 71 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU A 40 " --> pdb=" O LYS A 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.298A pdb=" N SER A 159 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL A 211 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY A 195 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LYS A 220 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU A 193 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N SER A 200 " --> pdb=" O TYR G 59 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N TYR G 59 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ALA G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N MET G 34 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER G 122 " --> pdb=" O VAL G 12 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.298A pdb=" N SER A 159 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL A 211 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY A 195 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LYS A 220 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU A 193 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N SER A 200 " --> pdb=" O TYR G 59 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N TYR G 59 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ALA G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N MET G 34 " --> pdb=" O ALA G 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 81 through 83 removed outlier: 4.597A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.668A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL B 106 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ARG B 129 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N THR B 176 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE B 42 " --> pdb=" O THR B 176 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.969A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 95 through 98 removed outlier: 4.039A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLU C 150 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N SER C 116 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 95 through 98 removed outlier: 4.039A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLU C 71 " --> pdb=" O PRO C 64 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASP C 75 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR C 83 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU C 52 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 9.913A pdb=" N THR C 51 " --> pdb=" O TYR C 181 " (cutoff:3.500A) removed outlier: 10.851A pdb=" N TRP C 183 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 9.570A pdb=" N ILE C 53 " --> pdb=" O TRP C 183 " (cutoff:3.500A) removed outlier: 10.561A pdb=" N ARG C 185 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 10.410A pdb=" N THR C 55 " --> pdb=" O ARG C 185 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N SER C 187 " --> pdb=" O THR C 55 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.609A pdb=" N SER C 171 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL C 221 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY C 205 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER C 230 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N PHE C 203 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 83 through 86 removed outlier: 4.649A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLU D 59 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE D 46 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 108 through 109 removed outlier: 7.167A pdb=" N GLU D 59 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE D 46 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.377A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 81 through 83 removed outlier: 4.444A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASP E 56 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL E 50 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TYR E 62 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE E 44 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N GLN E 64 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE E 42 " --> pdb=" O GLN E 64 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N TYR E 66 " --> pdb=" O MET E 40 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N MET E 40 " --> pdb=" O TYR E 66 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N ARG E 68 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N VAL E 38 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.775A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL E 106 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ARG E 129 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASP E 56 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL E 50 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TYR E 62 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE E 44 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N GLN E 64 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE E 42 " --> pdb=" O GLN E 64 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N TYR E 66 " --> pdb=" O MET E 40 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N MET E 40 " --> pdb=" O TYR E 66 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N ARG E 68 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N VAL E 38 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N THR E 176 " --> pdb=" O MET E 40 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE E 42 " --> pdb=" O THR E 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 96 through 98 removed outlier: 4.060A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 3 through 7 852 hydrogen bonds defined for protein. 2439 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: 1.94 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 2275 1.27 - 1.41: 4213 1.41 - 1.54: 9010 1.54 - 1.68: 47 1.68 - 1.81: 141 Bond restraints: 15686 Sorted by residual: bond pdb=" O4 PIO D 503 " pdb=" P4 PIO D 503 " ideal model delta sigma weight residual 1.710 1.595 0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" O4 PIO A 501 " pdb=" P4 PIO A 501 " ideal model delta sigma weight residual 1.710 1.596 0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" O5 PIO A 501 " pdb=" P5 PIO A 501 " ideal model delta sigma weight residual 1.699 1.608 0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" O5 PIO D 503 " pdb=" P5 PIO D 503 " ideal model delta sigma weight residual 1.699 1.610 0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" O13 PIO D 503 " pdb=" P1 PIO D 503 " ideal model delta sigma weight residual 1.651 1.591 0.060 2.00e-02 2.50e+03 8.91e+00 ... (remaining 15681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 21025 2.11 - 4.22: 238 4.22 - 6.34: 39 6.34 - 8.45: 6 8.45 - 10.56: 2 Bond angle restraints: 21310 Sorted by residual: angle pdb=" C4 PIO D 503 " pdb=" O4 PIO D 503 " pdb=" P4 PIO D 503 " ideal model delta sigma weight residual 121.90 132.46 -10.56 3.00e+00 1.11e-01 1.24e+01 angle pdb=" C4 PIO A 501 " pdb=" O4 PIO A 501 " pdb=" P4 PIO A 501 " ideal model delta sigma weight residual 121.90 132.33 -10.43 3.00e+00 1.11e-01 1.21e+01 angle pdb=" N VAL G 63 " pdb=" CA VAL G 63 " pdb=" C VAL G 63 " ideal model delta sigma weight residual 112.43 110.31 2.12 9.20e-01 1.18e+00 5.33e+00 angle pdb=" N GLY B 171 " pdb=" CA GLY B 171 " pdb=" C GLY B 171 " ideal model delta sigma weight residual 113.18 118.46 -5.28 2.37e+00 1.78e-01 4.96e+00 angle pdb=" C1 BMA d 3 " pdb=" O5 BMA d 3 " pdb=" C5 BMA d 3 " ideal model delta sigma weight residual 118.82 112.29 6.53 3.00e+00 1.11e-01 4.74e+00 ... (remaining 21305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 8596 16.88 - 33.76: 307 33.76 - 50.64: 46 50.64 - 67.52: 11 67.52 - 84.40: 4 Dihedral angle restraints: 8964 sinusoidal: 3622 harmonic: 5342 Sorted by residual: dihedral pdb=" CA ILE C 76 " pdb=" C ILE C 76 " pdb=" N PHE C 77 " pdb=" CA PHE C 77 " ideal model delta harmonic sigma weight residual 180.00 158.78 21.22 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA GLY B 170 " pdb=" C GLY B 170 " pdb=" N GLY B 171 " pdb=" CA GLY B 171 " ideal model delta harmonic sigma weight residual -180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA VAL A 64 " pdb=" C VAL A 64 " pdb=" N PHE A 65 " pdb=" CA PHE A 65 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 8961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2146 0.059 - 0.118: 296 0.118 - 0.177: 22 0.177 - 0.237: 5 0.237 - 0.296: 6 Chirality restraints: 2475 Sorted by residual: chirality pdb=" C1 BMA d 3 " pdb=" O4 NAG d 2 " pdb=" C2 BMA d 3 " pdb=" O5 BMA d 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-02 2.50e+03 2.16e+02 chirality pdb=" C1 MAN a 4 " pdb=" O3 BMA a 3 " pdb=" C2 MAN a 4 " pdb=" O5 MAN a 4 " both_signs ideal model delta sigma weight residual False 2.40 2.17 0.23 2.00e-02 2.50e+03 1.28e+02 chirality pdb=" C1 MAN a 7 " pdb=" O6 BMA a 3 " pdb=" C2 MAN a 7 " pdb=" O5 MAN a 7 " both_signs ideal model delta sigma weight residual False 2.40 2.17 0.23 2.00e-02 2.50e+03 1.27e+02 ... (remaining 2472 not shown) Planarity restraints: 2592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 EIE D 502 " -0.145 2.00e-02 2.50e+03 1.47e-01 5.91e+02 pdb=" C11 EIE D 502 " -0.150 2.00e-02 2.50e+03 pdb=" C12 EIE D 502 " -0.072 2.00e-02 2.50e+03 pdb=" C13 EIE D 502 " 0.016 2.00e-02 2.50e+03 pdb=" C7 EIE D 502 " 0.170 2.00e-02 2.50e+03 pdb=" C8 EIE D 502 " 0.031 2.00e-02 2.50e+03 pdb=" C9 EIE D 502 " -0.055 2.00e-02 2.50e+03 pdb=" N1 EIE D 502 " -0.236 2.00e-02 2.50e+03 pdb=" N2 EIE D 502 " 0.068 2.00e-02 2.50e+03 pdb=" N3 EIE D 502 " 0.298 2.00e-02 2.50e+03 pdb=" N4 EIE D 502 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.031 2.00e-02 2.50e+03 2.54e-02 8.04e+00 pdb=" C7 NAG F 1 " 0.010 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.024 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.040 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.018 2.00e-02 2.50e+03 1.46e-02 2.67e+00 pdb=" C7 NAG H 1 " 0.007 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " -0.014 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.022 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.002 2.00e-02 2.50e+03 ... (remaining 2589 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2560 2.77 - 3.30: 13980 3.30 - 3.83: 26284 3.83 - 4.37: 32654 4.37 - 4.90: 54860 Nonbonded interactions: 130338 Sorted by model distance: nonbonded pdb=" O VAL A 257 " pdb=" OG1 THR A 261 " model vdw 2.237 3.040 nonbonded pdb=" ND2AASN E 41 " pdb=" O ARG E 169 " model vdw 2.287 3.120 nonbonded pdb=" OE1 GLU E 153 " pdb=" OG SER E 209 " model vdw 2.290 3.040 nonbonded pdb=" OG1 THR A 267 " pdb=" OH TYR A 294 " model vdw 2.297 3.040 nonbonded pdb=" O SER A 92 " pdb=" NH1 ARG E 86 " model vdw 2.304 3.120 ... (remaining 130333 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 66 or resid 68 through 101 or resid 103 through \ 320 or resid 384 through 418)) selection = (chain 'D' and (resid 13 through 66 or resid 68 through 101 or resid 103 through \ 418)) } ncs_group { reference = (chain 'B' and (resid 10 through 40 or resid 42 through 65 or resid 67 through 3 \ 12 or resid 419 through 3101)) selection = (chain 'E' and (resid 10 through 40 or resid 42 through 65 or resid 67 through 3 \ 201)) } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'b' selection = chain 'e' } 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=0.50 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: 2.270 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.260 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 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 0.115 15722 Z= 0.190 Angle : 0.558 10.560 21413 Z= 0.247 Chirality : 0.044 0.296 2475 Planarity : 0.004 0.147 2585 Dihedral : 9.307 84.400 5519 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.25 % Allowed : 2.79 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: 0.58 (0.20), residues: 1791 helix: 0.88 (0.21), residues: 559 sheet: 0.32 (0.23), residues: 482 loop : 0.23 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 197 TYR 0.013 0.001 TYR B 277 PHE 0.010 0.001 PHE C 113 TRP 0.008 0.001 TRP B 426 HIS 0.003 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.19 (15686) covalent geometry : angle 0.55148 / 0.25 (21310) SS BOND : bond 0.00153 / 0.07 ( 5) SS BOND : angle 0.55921 / 0.36 ( 10) hydrogen bonds : bond 0.20833 / 13.76 ( 737) hydrogen bonds : angle 7.69323 / 5.32 ( 2439) link_ALPHA1-2 : bond 0.00273 / 0.14 ( 2) link_ALPHA1-2 : angle 0.52615 / 0.26 ( 6) link_ALPHA1-3 : bond 0.00240 / 0.14 ( 7) link_ALPHA1-3 : angle 1.34239 / 0.93 ( 21) link_ALPHA1-6 : bond 0.00265 / 0.12 ( 5) link_ALPHA1-6 : angle 1.09546 / 0.64 ( 15) link_BETA1-4 : bond 0.00241 / 0.13 ( 10) link_BETA1-4 : angle 1.39691 / 0.94 ( 30) link_NAG-ASN : bond 0.00392 / 0.18 ( 7) link_NAG-ASN : angle 1.87503 / 1.31 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 421 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 THR cc_start: 0.8990 (m) cc_final: 0.8716 (p) REVERT: A 17 ARG cc_start: 0.7576 (ttm170) cc_final: 0.7320 (ttm-80) REVERT: A 112 MET cc_start: 0.9012 (tpp) cc_final: 0.8688 (tpp) REVERT: B 13 LYS cc_start: 0.8338 (tttp) cc_final: 0.7836 (ttpt) REVERT: B 17 ASP cc_start: 0.7827 (m-30) cc_final: 0.7372 (m-30) REVERT: B 269 ARG cc_start: 0.8241 (ttt180) cc_final: 0.8020 (ttt180) REVERT: C 97 ARG cc_start: 0.8303 (mtt-85) cc_final: 0.7925 (mtt-85) REVERT: C 150 GLU cc_start: 0.7791 (tt0) cc_final: 0.7292 (tm-30) REVERT: C 197 ARG cc_start: 0.7548 (mtp180) cc_final: 0.7304 (mtm180) REVERT: C 211 GLU cc_start: 0.7440 (pt0) cc_final: 0.7032 (pm20) REVERT: C 223 MET cc_start: 0.8981 (mmm) cc_final: 0.8613 (mmm) REVERT: C 413 TYR cc_start: 0.7636 (m-10) cc_final: 0.7356 (m-10) REVERT: D 18 ILE cc_start: 0.8437 (mt) cc_final: 0.8172 (mm) REVERT: E 86 ARG cc_start: 0.8405 (mtm180) cc_final: 0.8144 (mtm110) REVERT: E 90 GLN cc_start: 0.8523 (mt0) cc_final: 0.8315 (mp10) REVERT: E 269 ARG cc_start: 0.8174 (ttt180) cc_final: 0.7908 (ttt180) REVERT: G 19 ARG cc_start: 0.8584 (ttt90) cc_final: 0.8163 (ttt-90) outliers start: 4 outliers final: 2 residues processed: 424 average time/residue: 0.6043 time to fit residues: 280.0111 Evaluate side-chains 308 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 306 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 222 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN A 229 GLN B 265 ASN B 421 ASN C 60 ASN C 80 GLN C 182 GLN C 426 ASN D 68 GLN D 116 ASN D 190 GLN D 229 GLN D 408 ASN E 107 HIS E 119 HIS E 243 ASN E 265 ASN E 312 GLN G 81 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.126475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.098093 restraints weight = 38736.175| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.10 r_work: 0.2752 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15722 Z= 0.163 Angle : 0.578 7.881 21413 Z= 0.301 Chirality : 0.043 0.188 2475 Planarity : 0.005 0.049 2585 Dihedral : 5.243 62.366 2122 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.54 % Allowed : 11.83 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: 1.05 (0.20), residues: 1791 helix: 1.91 (0.21), residues: 559 sheet: 0.27 (0.23), residues: 463 loop : 0.18 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 313 TYR 0.023 0.002 TYR E 299 PHE 0.014 0.002 PHE A 304 TRP 0.011 0.001 TRP D 317 HIS 0.005 0.001 HIS D 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (15686) covalent geometry : angle 0.56972 / 0.30 (21310) SS BOND : bond 0.00411 / 0.19 ( 5) SS BOND : angle 0.92055 / 0.62 ( 10) hydrogen bonds : bond 0.04851 / 3.17 ( 737) hydrogen bonds : angle 5.29580 / 3.68 ( 2439) link_ALPHA1-2 : bond 0.00534 / 0.27 ( 2) link_ALPHA1-2 : angle 1.44950 / 0.76 ( 6) link_ALPHA1-3 : bond 0.00541 / 0.27 ( 7) link_ALPHA1-3 : angle 1.56452 / 1.00 ( 21) link_ALPHA1-6 : bond 0.00726 / 0.40 ( 5) link_ALPHA1-6 : angle 1.46196 / 0.85 ( 15) link_BETA1-4 : bond 0.00403 / 0.19 ( 10) link_BETA1-4 : angle 1.38430 / 0.91 ( 30) link_NAG-ASN : bond 0.00199 / 0.11 ( 7) link_NAG-ASN : angle 1.74345 / 1.23 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 311 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 THR cc_start: 0.7564 (p) cc_final: 0.7203 (t) REVERT: A 17 ARG cc_start: 0.7856 (ttm170) cc_final: 0.7354 (ttm110) REVERT: A 114 MET cc_start: 0.8487 (mmm) cc_final: 0.8166 (mmm) REVERT: A 315 TYR cc_start: 0.8791 (p90) cc_final: 0.8483 (p90) REVERT: B 13 LYS cc_start: 0.8219 (tttp) cc_final: 0.7609 (ttpt) REVERT: B 17 ASP cc_start: 0.8268 (m-30) cc_final: 0.7670 (m-30) REVERT: B 103 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8304 (ttmt) REVERT: B 269 ARG cc_start: 0.8514 (ttt180) cc_final: 0.8239 (ttt180) REVERT: B 283 MET cc_start: 0.8360 (mmm) cc_final: 0.8065 (mmm) REVERT: B 421 ASN cc_start: 0.7780 (OUTLIER) cc_final: 0.7517 (t0) REVERT: C 70 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.6908 (mpp) REVERT: C 97 ARG cc_start: 0.8686 (mtt-85) cc_final: 0.8341 (mtt180) REVERT: C 211 GLU cc_start: 0.8247 (pt0) cc_final: 0.7590 (pm20) REVERT: C 223 MET cc_start: 0.9141 (mmm) cc_final: 0.8827 (mmm) REVERT: C 232 ARG cc_start: 0.8388 (mtm180) cc_final: 0.7951 (ptp-170) REVERT: C 413 TYR cc_start: 0.7576 (m-10) cc_final: 0.7263 (m-10) REVERT: D 63 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.7931 (m-30) REVERT: D 82 THR cc_start: 0.7975 (p) cc_final: 0.7758 (m) REVERT: D 204 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7989 (mt0) REVERT: D 402 LEU cc_start: 0.8206 (tp) cc_final: 0.7898 (tt) REVERT: E 90 GLN cc_start: 0.8740 (mt0) cc_final: 0.8471 (mp10) REVERT: E 179 GLU cc_start: 0.7954 (pm20) cc_final: 0.7626 (mp0) REVERT: G 19 ARG cc_start: 0.8705 (ttt90) cc_final: 0.8489 (ttt-90) REVERT: G 81 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7475 (tm130) outliers start: 41 outliers final: 9 residues processed: 323 average time/residue: 0.6177 time to fit residues: 218.3308 Evaluate side-chains 311 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 296 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain G residue 81 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 128 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 169 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN A 242 GLN A 275 ASN B 265 ASN C 182 GLN D 408 ASN E 265 ASN G 81 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.125540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.097425 restraints weight = 41337.949| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.35 r_work: 0.2722 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15722 Z= 0.176 Angle : 0.564 7.550 21413 Z= 0.292 Chirality : 0.043 0.192 2475 Planarity : 0.004 0.046 2585 Dihedral : 5.321 65.510 2119 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.91 % Allowed : 12.39 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: 1.09 (0.20), residues: 1791 helix: 2.06 (0.21), residues: 557 sheet: 0.25 (0.23), residues: 474 loop : 0.14 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 187 TYR 0.028 0.002 TYR E 299 PHE 0.015 0.002 PHE A 304 TRP 0.015 0.001 TRP D 317 HIS 0.005 0.001 HIS D 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (15686) covalent geometry : angle 0.55568 / 0.29 (21310) SS BOND : bond 0.00395 / 0.19 ( 5) SS BOND : angle 0.86162 / 0.58 ( 10) hydrogen bonds : bond 0.04452 / 2.91 ( 737) hydrogen bonds : angle 5.03726 / 3.49 ( 2439) link_ALPHA1-2 : bond 0.00351 / 0.17 ( 2) link_ALPHA1-2 : angle 1.69951 / 0.88 ( 6) link_ALPHA1-3 : bond 0.00449 / 0.22 ( 7) link_ALPHA1-3 : angle 1.55434 / 0.99 ( 21) link_ALPHA1-6 : bond 0.00599 / 0.34 ( 5) link_ALPHA1-6 : angle 1.51812 / 0.89 ( 15) link_BETA1-4 : bond 0.00363 / 0.19 ( 10) link_BETA1-4 : angle 1.38706 / 0.92 ( 30) link_NAG-ASN : bond 0.00224 / 0.12 ( 7) link_NAG-ASN : angle 1.77868 / 1.25 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 306 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7888 (ttm170) cc_final: 0.7606 (ttp-110) REVERT: A 112 MET cc_start: 0.9152 (tpp) cc_final: 0.8849 (tpp) REVERT: A 286 MET cc_start: 0.8449 (ttm) cc_final: 0.8012 (tpp) REVERT: A 315 TYR cc_start: 0.8861 (p90) cc_final: 0.8492 (p90) REVERT: B 13 LYS cc_start: 0.8250 (tttp) cc_final: 0.7627 (ttpt) REVERT: B 17 ASP cc_start: 0.8339 (m-30) cc_final: 0.7730 (m-30) REVERT: B 70 LYS cc_start: 0.8656 (mtpt) cc_final: 0.8174 (mmtm) REVERT: B 103 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8323 (ttmt) REVERT: B 227 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7915 (mmm) REVERT: B 269 ARG cc_start: 0.8511 (ttt180) cc_final: 0.8242 (ttt180) REVERT: B 283 MET cc_start: 0.8409 (mmm) cc_final: 0.8087 (mmm) REVERT: C 97 ARG cc_start: 0.8615 (mtt-85) cc_final: 0.8342 (mtt180) REVERT: C 102 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8506 (mtm) REVERT: C 211 GLU cc_start: 0.8367 (pt0) cc_final: 0.7716 (pm20) REVERT: C 214 LYS cc_start: 0.8440 (tptt) cc_final: 0.8210 (mptt) REVERT: C 223 MET cc_start: 0.9148 (mmm) cc_final: 0.8838 (mmm) REVERT: C 232 ARG cc_start: 0.8391 (mtm180) cc_final: 0.7935 (ptp-170) REVERT: C 413 TYR cc_start: 0.7671 (m-10) cc_final: 0.7288 (m-10) REVERT: D 63 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8001 (m-30) REVERT: D 114 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7457 (pmt) REVERT: D 204 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8013 (mt0) REVERT: D 402 LEU cc_start: 0.8247 (tp) cc_final: 0.7938 (tt) REVERT: E 49 MET cc_start: 0.8518 (tpp) cc_final: 0.7022 (tmt) REVERT: E 90 GLN cc_start: 0.8729 (mt0) cc_final: 0.8412 (mp10) REVERT: E 179 GLU cc_start: 0.8061 (pm20) cc_final: 0.7710 (mp0) REVERT: E 274 LYS cc_start: 0.7753 (mmtm) cc_final: 0.7490 (mmtt) REVERT: G 5 GLN cc_start: 0.7103 (pp30) cc_final: 0.6870 (pp30) outliers start: 47 outliers final: 18 residues processed: 321 average time/residue: 0.6243 time to fit residues: 219.1816 Evaluate side-chains 310 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 286 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain G residue 81 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 44 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 166 optimal weight: 0.0570 chunk 133 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 102 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 128 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 GLN A 275 ASN B 265 ASN C 182 GLN E 265 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.127205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.099887 restraints weight = 33500.058| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.58 r_work: 0.2791 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15722 Z= 0.117 Angle : 0.517 6.921 21413 Z= 0.269 Chirality : 0.041 0.176 2475 Planarity : 0.004 0.041 2585 Dihedral : 5.129 64.283 2119 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.48 % Allowed : 13.51 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: 1.21 (0.20), residues: 1791 helix: 2.24 (0.21), residues: 557 sheet: 0.26 (0.23), residues: 474 loop : 0.17 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 169 TYR 0.028 0.001 TYR E 299 PHE 0.015 0.001 PHE D 310 TRP 0.016 0.001 TRP D 317 HIS 0.003 0.001 HIS D 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (15686) covalent geometry : angle 0.50921 / 0.27 (21310) SS BOND : bond 0.00267 / 0.13 ( 5) SS BOND : angle 0.62364 / 0.41 ( 10) hydrogen bonds : bond 0.03814 / 2.50 ( 737) hydrogen bonds : angle 4.75821 / 3.29 ( 2439) link_ALPHA1-2 : bond 0.00484 / 0.24 ( 2) link_ALPHA1-2 : angle 1.61415 / 0.85 ( 6) link_ALPHA1-3 : bond 0.00526 / 0.27 ( 7) link_ALPHA1-3 : angle 1.44393 / 0.94 ( 21) link_ALPHA1-6 : bond 0.00651 / 0.37 ( 5) link_ALPHA1-6 : angle 1.44893 / 0.84 ( 15) link_BETA1-4 : bond 0.00331 / 0.18 ( 10) link_BETA1-4 : angle 1.34395 / 0.89 ( 30) link_NAG-ASN : bond 0.00144 / 0.08 ( 7) link_NAG-ASN : angle 1.65820 / 1.16 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 300 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7987 (ttm170) cc_final: 0.7725 (ttp-110) REVERT: A 286 MET cc_start: 0.8525 (ttm) cc_final: 0.8186 (tpp) REVERT: A 315 TYR cc_start: 0.8942 (p90) cc_final: 0.8589 (p90) REVERT: B 13 LYS cc_start: 0.8327 (tttp) cc_final: 0.7701 (ttpt) REVERT: B 17 ASP cc_start: 0.8445 (m-30) cc_final: 0.7813 (m-30) REVERT: B 18 LYS cc_start: 0.8577 (tttt) cc_final: 0.8205 (ptpt) REVERT: B 49 MET cc_start: 0.8015 (mmp) cc_final: 0.7777 (mmm) REVERT: B 70 LYS cc_start: 0.8673 (mtpt) cc_final: 0.8221 (mmtm) REVERT: B 103 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8429 (ttmt) REVERT: B 227 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8075 (mmm) REVERT: B 269 ARG cc_start: 0.8597 (ttt180) cc_final: 0.8345 (mtp180) REVERT: B 286 MET cc_start: 0.8483 (tpt) cc_final: 0.8279 (tpt) REVERT: C 102 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8525 (mtm) REVERT: C 154 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.7920 (mp10) REVERT: C 211 GLU cc_start: 0.8577 (pt0) cc_final: 0.7914 (pm20) REVERT: C 214 LYS cc_start: 0.8510 (tptt) cc_final: 0.8232 (mptt) REVERT: C 223 MET cc_start: 0.9173 (mmm) cc_final: 0.8938 (mmm) REVERT: C 232 ARG cc_start: 0.8378 (mtm180) cc_final: 0.7968 (ptp-170) REVERT: C 413 TYR cc_start: 0.7721 (m-10) cc_final: 0.7284 (m-10) REVERT: D 13 THR cc_start: 0.6262 (m) cc_final: 0.6042 (m) REVERT: D 63 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8195 (m-30) REVERT: D 81 MET cc_start: 0.6863 (OUTLIER) cc_final: 0.6598 (pmm) REVERT: D 204 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8034 (mt0) REVERT: D 220 LYS cc_start: 0.9108 (tttt) cc_final: 0.8839 (tttp) REVERT: D 402 LEU cc_start: 0.8271 (tp) cc_final: 0.7988 (tt) REVERT: E 90 GLN cc_start: 0.8833 (mt0) cc_final: 0.8530 (mp10) REVERT: E 179 GLU cc_start: 0.8260 (pm20) cc_final: 0.7864 (mp0) REVERT: E 215 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.7980 (tmtm) REVERT: E 421 ASN cc_start: 0.7316 (t0) cc_final: 0.7059 (t0) REVERT: G 5 GLN cc_start: 0.7256 (pp30) cc_final: 0.6991 (pp30) outliers start: 40 outliers final: 13 residues processed: 312 average time/residue: 0.6729 time to fit residues: 228.7890 Evaluate side-chains 313 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 292 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain G residue 81 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 116 optimal weight: 0.0270 chunk 55 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 137 optimal weight: 0.0870 chunk 52 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN A 275 ASN B 265 ASN B 421 ASN C 182 GLN E 265 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.127026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.098507 restraints weight = 39244.024| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.03 r_work: 0.2798 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15722 Z= 0.110 Angle : 0.503 8.683 21413 Z= 0.259 Chirality : 0.041 0.168 2475 Planarity : 0.004 0.067 2585 Dihedral : 5.060 62.333 2119 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.23 % Allowed : 14.44 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: 1.27 (0.20), residues: 1791 helix: 2.34 (0.21), residues: 557 sheet: 0.30 (0.23), residues: 473 loop : 0.18 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 169 TYR 0.028 0.001 TYR E 299 PHE 0.014 0.001 PHE D 310 TRP 0.019 0.001 TRP D 317 HIS 0.003 0.001 HIS A 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (15686) covalent geometry : angle 0.49503 / 0.26 (21310) SS BOND : bond 0.00243 / 0.12 ( 5) SS BOND : angle 0.58930 / 0.39 ( 10) hydrogen bonds : bond 0.03541 / 2.32 ( 737) hydrogen bonds : angle 4.56278 / 3.16 ( 2439) link_ALPHA1-2 : bond 0.00497 / 0.25 ( 2) link_ALPHA1-2 : angle 1.63571 / 0.86 ( 6) link_ALPHA1-3 : bond 0.00532 / 0.27 ( 7) link_ALPHA1-3 : angle 1.44385 / 0.94 ( 21) link_ALPHA1-6 : bond 0.00623 / 0.35 ( 5) link_ALPHA1-6 : angle 1.42664 / 0.82 ( 15) link_BETA1-4 : bond 0.00331 / 0.18 ( 10) link_BETA1-4 : angle 1.32852 / 0.88 ( 30) link_NAG-ASN : bond 0.00130 / 0.07 ( 7) link_NAG-ASN : angle 1.57449 / 1.10 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 295 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7888 (ttm170) cc_final: 0.7535 (ttp-110) REVERT: A 315 TYR cc_start: 0.8861 (p90) cc_final: 0.8517 (p90) REVERT: B 13 LYS cc_start: 0.8209 (tttp) cc_final: 0.8005 (ttpt) REVERT: B 18 LYS cc_start: 0.8495 (tttt) cc_final: 0.8157 (ptpt) REVERT: B 70 LYS cc_start: 0.8593 (mtpt) cc_final: 0.8144 (mmtm) REVERT: B 103 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8327 (ttmt) REVERT: B 283 MET cc_start: 0.8250 (mmm) cc_final: 0.7985 (mmt) REVERT: C 154 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7851 (mp10) REVERT: C 211 GLU cc_start: 0.8363 (pt0) cc_final: 0.7734 (pm20) REVERT: C 214 LYS cc_start: 0.8415 (tptt) cc_final: 0.8177 (mptt) REVERT: C 223 MET cc_start: 0.9107 (mmm) cc_final: 0.8771 (mmm) REVERT: C 232 ARG cc_start: 0.8336 (mtm180) cc_final: 0.7879 (ptp-170) REVERT: C 413 TYR cc_start: 0.7671 (m-10) cc_final: 0.7444 (m-10) REVERT: D 13 THR cc_start: 0.6229 (m) cc_final: 0.6027 (m) REVERT: D 63 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7927 (m-30) REVERT: D 114 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7167 (pmt) REVERT: D 204 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7902 (mt0) REVERT: D 220 LYS cc_start: 0.8989 (tttt) cc_final: 0.8687 (tttp) REVERT: D 402 LEU cc_start: 0.8223 (tp) cc_final: 0.7955 (tt) REVERT: E 70 LYS cc_start: 0.8610 (mttt) cc_final: 0.8261 (mtpm) REVERT: E 90 GLN cc_start: 0.8732 (mt0) cc_final: 0.8432 (mp10) REVERT: E 179 GLU cc_start: 0.8011 (pm20) cc_final: 0.7671 (mp0) REVERT: E 215 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.7898 (tmtm) REVERT: E 421 ASN cc_start: 0.7315 (t0) cc_final: 0.7040 (t0) REVERT: G 5 GLN cc_start: 0.7205 (pp30) cc_final: 0.6958 (pp30) outliers start: 36 outliers final: 12 residues processed: 307 average time/residue: 0.6945 time to fit residues: 232.2996 Evaluate side-chains 303 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 285 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 444 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.054 > 50: distance: 107 - 116: 11.163 distance: 117 - 118: 8.589 distance: 117 - 120: 16.609 distance: 118 - 119: 22.084 distance: 118 - 125: 30.741 distance: 120 - 121: 13.606 distance: 121 - 122: 16.296 distance: 122 - 123: 16.077 distance: 123 - 124: 6.713 distance: 125 - 126: 14.087 distance: 126 - 127: 15.653 distance: 126 - 129: 24.288 distance: 127 - 128: 52.990 distance: 127 - 131: 10.115 distance: 129 - 130: 46.022 distance: 131 - 132: 7.702 distance: 132 - 133: 27.618 distance: 132 - 135: 43.223 distance: 133 - 134: 33.228 distance: 133 - 139: 24.411 distance: 135 - 136: 15.831 distance: 136 - 137: 37.273 distance: 136 - 138: 32.717 distance: 139 - 140: 18.098 distance: 139 - 145: 40.939 distance: 140 - 141: 10.391 distance: 140 - 143: 31.466 distance: 141 - 142: 25.489 distance: 141 - 146: 8.962 distance: 143 - 144: 24.238 distance: 144 - 145: 12.065 distance: 146 - 147: 15.310 distance: 147 - 148: 20.318 distance: 147 - 150: 23.190 distance: 148 - 149: 19.577 distance: 148 - 155: 18.944 distance: 150 - 151: 19.341 distance: 151 - 152: 32.757 distance: 152 - 153: 11.959 distance: 153 - 154: 38.443 distance: 155 - 156: 16.551 distance: 156 - 157: 18.060 distance: 156 - 159: 9.306 distance: 157 - 158: 14.642 distance: 157 - 162: 18.245 distance: 159 - 160: 18.889 distance: 159 - 161: 24.604 distance: 162 - 163: 17.305 distance: 163 - 164: 12.543 distance: 163 - 166: 21.732 distance: 164 - 165: 13.681 distance: 164 - 168: 23.125 distance: 166 - 167: 48.780 distance: 168 - 169: 12.349 distance: 169 - 170: 26.688 distance: 169 - 172: 15.716 distance: 170 - 171: 4.292 distance: 170 - 180: 7.993 distance: 172 - 173: 11.347 distance: 173 - 174: 13.303 distance: 173 - 175: 5.220 distance: 174 - 176: 10.788 distance: 175 - 177: 11.631 distance: 176 - 178: 5.555 distance: 177 - 178: 12.836 distance: 178 - 179: 14.824 distance: 180 - 181: 11.017 distance: 181 - 182: 17.495 distance: 181 - 184: 17.904 distance: 182 - 183: 23.919 distance: 182 - 187: 23.889 distance: 184 - 185: 44.679 distance: 184 - 186: 12.138 distance: 187 - 188: 17.089 distance: 188 - 189: 18.787 distance: 188 - 191: 42.687 distance: 189 - 190: 6.185 distance: 189 - 194: 6.519 distance: 190 - 211: 3.450 distance: 191 - 192: 14.652 distance: 191 - 193: 17.894