Starting phenix.real_space_refine on Thu Feb 5 18:42:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e64_47549/02_2026/9e64_47549.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e64_47549/02_2026/9e64_47549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e64_47549/02_2026/9e64_47549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e64_47549/02_2026/9e64_47549.map" model { file = "/net/cci-nas-00/data/ceres_data/9e64_47549/02_2026/9e64_47549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e64_47549/02_2026/9e64_47549.cif" } resolution = 3.0 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= 0.001 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 35 5.49 5 S 70 5.16 5 C 12488 2.51 5 N 2982 2.21 5 O 3444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19019 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2509 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 8, 'TRANS': 322} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "G" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2509 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 8, 'TRANS': 322} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "A" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 208 Unusual residues: {'PTY': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Chain: "G" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 208 Unusual residues: {'PTY': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 2.62, per 1000 atoms: 0.14 Number of scatterers: 19019 At special positions: 0 Unit cell: (109.22, 107.5, 141.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 P 35 15.00 O 3444 8.00 N 2982 7.00 C 12488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 82 " - pdb=" SG CYS B 82 " distance=0.00 Simple disulfide: pdb=" SG CYS B 292 " - pdb=" SG CYS B 292 " distance=0.00 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 739.3 milliseconds 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4312 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 15 sheets defined 62.2% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.542A pdb=" N LEU A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 32 removed outlier: 4.538A pdb=" N PHE A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N CYS A 20 " --> pdb=" O ILE A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 68 removed outlier: 3.564A pdb=" N ILE A 65 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 109 removed outlier: 4.151A pdb=" N ILE A 78 " --> pdb=" O THR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 134 Processing helix chain 'A' and resid 143 through 160 Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 219 through 223 Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 244 through 249 removed outlier: 3.746A pdb=" N ALA A 248 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ALA A 249 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 264 Processing helix chain 'A' and resid 298 through 320 removed outlier: 3.579A pdb=" N HIS A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 13 removed outlier: 3.542A pdb=" N LEU B 13 " --> pdb=" O ASN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 32 removed outlier: 4.539A pdb=" N PHE B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N CYS B 20 " --> pdb=" O ILE B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 68 removed outlier: 3.564A pdb=" N ILE B 65 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 109 removed outlier: 4.151A pdb=" N ILE B 78 " --> pdb=" O THR B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 134 Processing helix chain 'B' and resid 143 through 160 Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 219 through 223 Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 244 through 249 removed outlier: 3.746A pdb=" N ALA B 248 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ALA B 249 " --> pdb=" O GLU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 264 Processing helix chain 'B' and resid 298 through 320 removed outlier: 3.579A pdb=" N HIS B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 13 removed outlier: 3.543A pdb=" N LEU C 13 " --> pdb=" O ASN C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 32 removed outlier: 4.538A pdb=" N PHE C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N CYS C 20 " --> pdb=" O ILE C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 68 removed outlier: 3.564A pdb=" N ILE C 65 " --> pdb=" O ILE C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 109 removed outlier: 4.150A pdb=" N ILE C 78 " --> pdb=" O THR C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 134 Processing helix chain 'C' and resid 143 through 160 Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 219 through 223 Processing helix chain 'C' and resid 229 through 232 Processing helix chain 'C' and resid 244 through 249 removed outlier: 3.746A pdb=" N ALA C 248 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ALA C 249 " --> pdb=" O GLU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 264 Processing helix chain 'C' and resid 298 through 320 removed outlier: 3.579A pdb=" N HIS C 320 " --> pdb=" O ILE C 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 13 removed outlier: 3.543A pdb=" N LEU D 13 " --> pdb=" O ASN D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 32 removed outlier: 4.538A pdb=" N PHE D 17 " --> pdb=" O LEU D 13 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N CYS D 20 " --> pdb=" O ILE D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 68 removed outlier: 3.564A pdb=" N ILE D 65 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 109 removed outlier: 4.150A pdb=" N ILE D 78 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 134 Processing helix chain 'D' and resid 143 through 160 Processing helix chain 'D' and resid 160 through 176 Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 229 through 232 Processing helix chain 'D' and resid 244 through 249 removed outlier: 3.747A pdb=" N ALA D 248 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ALA D 249 " --> pdb=" O GLU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 264 Processing helix chain 'D' and resid 298 through 320 removed outlier: 3.579A pdb=" N HIS D 320 " --> pdb=" O ILE D 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 13 removed outlier: 3.542A pdb=" N LEU E 13 " --> pdb=" O ASN E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 32 removed outlier: 4.539A pdb=" N PHE E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N CYS E 20 " --> pdb=" O ILE E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 68 removed outlier: 3.564A pdb=" N ILE E 65 " --> pdb=" O ILE E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 109 removed outlier: 4.151A pdb=" N ILE E 78 " --> pdb=" O THR E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 134 Processing helix chain 'E' and resid 143 through 160 Processing helix chain 'E' and resid 160 through 176 Processing helix chain 'E' and resid 219 through 223 Processing helix chain 'E' and resid 229 through 232 Processing helix chain 'E' and resid 244 through 249 removed outlier: 3.746A pdb=" N ALA E 248 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ALA E 249 " --> pdb=" O GLU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 264 Processing helix chain 'E' and resid 298 through 320 removed outlier: 3.579A pdb=" N HIS E 320 " --> pdb=" O ILE E 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 13 removed outlier: 3.542A pdb=" N LEU F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 32 removed outlier: 4.539A pdb=" N PHE F 17 " --> pdb=" O LEU F 13 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N CYS F 20 " --> pdb=" O ILE F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 68 removed outlier: 3.564A pdb=" N ILE F 65 " --> pdb=" O ILE F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 109 removed outlier: 4.151A pdb=" N ILE F 78 " --> pdb=" O THR F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 134 Processing helix chain 'F' and resid 143 through 160 Processing helix chain 'F' and resid 160 through 176 Processing helix chain 'F' and resid 219 through 223 Processing helix chain 'F' and resid 229 through 232 Processing helix chain 'F' and resid 244 through 249 removed outlier: 3.746A pdb=" N ALA F 248 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ALA F 249 " --> pdb=" O GLU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 264 Processing helix chain 'F' and resid 298 through 320 removed outlier: 3.579A pdb=" N HIS F 320 " --> pdb=" O ILE F 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 13 removed outlier: 3.543A pdb=" N LEU G 13 " --> pdb=" O ASN G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 32 removed outlier: 4.538A pdb=" N PHE G 17 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N CYS G 20 " --> pdb=" O ILE G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 68 removed outlier: 3.564A pdb=" N ILE G 65 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 109 removed outlier: 4.151A pdb=" N ILE G 78 " --> pdb=" O THR G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 134 Processing helix chain 'G' and resid 143 through 160 Processing helix chain 'G' and resid 160 through 176 Processing helix chain 'G' and resid 219 through 223 Processing helix chain 'G' and resid 229 through 232 Processing helix chain 'G' and resid 244 through 249 removed outlier: 3.746A pdb=" N ALA G 248 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ALA G 249 " --> pdb=" O GLU G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 264 Processing helix chain 'G' and resid 298 through 320 removed outlier: 3.579A pdb=" N HIS G 320 " --> pdb=" O ILE G 316 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 185 removed outlier: 6.608A pdb=" N LYS A 205 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE A 199 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 removed outlier: 7.393A pdb=" N ILE G 203 " --> pdb=" O ILE G 199 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE G 199 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS G 205 " --> pdb=" O ALA G 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 235 through 243 removed outlier: 3.861A pdb=" N ARG A 235 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A 280 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET A 289 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N PHE A 278 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N TYR A 291 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N VAL A 276 " --> pdb=" O TYR A 291 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 333 removed outlier: 8.503A pdb=" N GLN G 329 " --> pdb=" O SER A 328 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR A 330 " --> pdb=" O GLN G 329 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU G 331 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TYR A 332 " --> pdb=" O LEU G 331 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N MET G 333 " --> pdb=" O TYR A 332 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 184 through 185 removed outlier: 6.608A pdb=" N LYS B 205 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE B 199 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 235 through 243 removed outlier: 3.862A pdb=" N ARG B 235 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN B 280 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET B 289 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N PHE B 278 " --> pdb=" O MET B 289 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N TYR B 291 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL B 276 " --> pdb=" O TYR B 291 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 184 through 185 removed outlier: 6.608A pdb=" N LYS C 205 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE C 199 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 235 through 243 removed outlier: 3.861A pdb=" N ARG C 235 " --> pdb=" O THR C 294 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN C 280 " --> pdb=" O ASN C 287 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET C 289 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N PHE C 278 " --> pdb=" O MET C 289 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N TYR C 291 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N VAL C 276 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 184 through 185 removed outlier: 6.608A pdb=" N LYS D 205 " --> pdb=" O ALA D 197 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE D 199 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE D 203 " --> pdb=" O ILE D 199 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 235 through 243 removed outlier: 3.862A pdb=" N ARG D 235 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN D 280 " --> pdb=" O ASN D 287 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET D 289 " --> pdb=" O PHE D 278 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N PHE D 278 " --> pdb=" O MET D 289 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N TYR D 291 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N VAL D 276 " --> pdb=" O TYR D 291 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 184 through 185 removed outlier: 6.608A pdb=" N LYS E 205 " --> pdb=" O ALA E 197 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE E 199 " --> pdb=" O ILE E 203 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE E 203 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 235 through 243 removed outlier: 3.862A pdb=" N ARG E 235 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN E 280 " --> pdb=" O ASN E 287 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET E 289 " --> pdb=" O PHE E 278 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N PHE E 278 " --> pdb=" O MET E 289 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N TYR E 291 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N VAL E 276 " --> pdb=" O TYR E 291 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 184 through 185 removed outlier: 6.609A pdb=" N LYS F 205 " --> pdb=" O ALA F 197 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE F 199 " --> pdb=" O ILE F 203 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE F 203 " --> pdb=" O ILE F 199 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 235 through 243 removed outlier: 3.862A pdb=" N ARG F 235 " --> pdb=" O THR F 294 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN F 280 " --> pdb=" O ASN F 287 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET F 289 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N PHE F 278 " --> pdb=" O MET F 289 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N TYR F 291 " --> pdb=" O VAL F 276 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N VAL F 276 " --> pdb=" O TYR F 291 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 235 through 243 removed outlier: 3.861A pdb=" N ARG G 235 " --> pdb=" O THR G 294 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN G 280 " --> pdb=" O ASN G 287 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET G 289 " --> pdb=" O PHE G 278 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N PHE G 278 " --> pdb=" O MET G 289 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N TYR G 291 " --> pdb=" O VAL G 276 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL G 276 " --> pdb=" O TYR G 291 " (cutoff:3.500A) 1229 hydrogen bonds defined for protein. 3540 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.34 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3172 1.33 - 1.45: 4688 1.45 - 1.57: 11264 1.57 - 1.69: 70 1.69 - 1.81: 126 Bond restraints: 19320 Sorted by residual: bond pdb=" C8 PTY B 403 " pdb=" O7 PTY B 403 " ideal model delta sigma weight residual 1.331 1.455 -0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" C8 PTY F 403 " pdb=" O7 PTY F 403 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" C8 PTY G 401 " pdb=" O7 PTY G 401 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" C8 PTY E 403 " pdb=" O7 PTY E 403 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" C8 PTY D 403 " pdb=" O7 PTY D 403 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.76e+01 ... (remaining 19315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 25425 2.30 - 4.59: 375 4.59 - 6.89: 58 6.89 - 9.18: 35 9.18 - 11.48: 21 Bond angle restraints: 25914 Sorted by residual: angle pdb=" CA LYS F 103 " pdb=" CB LYS F 103 " pdb=" CG LYS F 103 " ideal model delta sigma weight residual 114.10 121.63 -7.53 2.00e+00 2.50e-01 1.42e+01 angle pdb=" CA LYS D 103 " pdb=" CB LYS D 103 " pdb=" CG LYS D 103 " ideal model delta sigma weight residual 114.10 121.63 -7.53 2.00e+00 2.50e-01 1.42e+01 angle pdb=" CA LYS A 103 " pdb=" CB LYS A 103 " pdb=" CG LYS A 103 " ideal model delta sigma weight residual 114.10 121.61 -7.51 2.00e+00 2.50e-01 1.41e+01 angle pdb=" CA LYS B 103 " pdb=" CB LYS B 103 " pdb=" CG LYS B 103 " ideal model delta sigma weight residual 114.10 121.61 -7.51 2.00e+00 2.50e-01 1.41e+01 angle pdb=" CA LYS E 103 " pdb=" CB LYS E 103 " pdb=" CG LYS E 103 " ideal model delta sigma weight residual 114.10 121.60 -7.50 2.00e+00 2.50e-01 1.41e+01 ... (remaining 25909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.77: 10409 19.77 - 39.53: 973 39.53 - 59.30: 298 59.30 - 79.07: 42 79.07 - 98.83: 14 Dihedral angle restraints: 11736 sinusoidal: 5037 harmonic: 6699 Sorted by residual: dihedral pdb=" CB CYS B 82 " pdb=" SG CYS B 82 " pdb=" SG CYS B 82 " pdb=" CB CYS B 82 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 dihedral pdb=" CB CYS B 292 " pdb=" SG CYS B 292 " pdb=" SG CYS B 292 " pdb=" CB CYS B 292 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 dihedral pdb=" CA PHE B 138 " pdb=" C PHE B 138 " pdb=" N GLY B 139 " pdb=" CA GLY B 139 " ideal model delta harmonic sigma weight residual -180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 11733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1884 0.030 - 0.060: 560 0.060 - 0.090: 341 0.090 - 0.120: 90 0.120 - 0.150: 58 Chirality restraints: 2933 Sorted by residual: chirality pdb=" CG LEU G 145 " pdb=" CB LEU G 145 " pdb=" CD1 LEU G 145 " pdb=" CD2 LEU G 145 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CG LEU B 145 " pdb=" CB LEU B 145 " pdb=" CD1 LEU B 145 " pdb=" CD2 LEU B 145 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CG LEU E 145 " pdb=" CB LEU E 145 " pdb=" CD1 LEU E 145 " pdb=" CD2 LEU E 145 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.45e-01 ... (remaining 2930 not shown) Planarity restraints: 3122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 102 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" CD GLU C 102 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU C 102 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU C 102 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 102 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" CD GLU E 102 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU E 102 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU E 102 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU F 102 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.13e+00 pdb=" CD GLU F 102 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU F 102 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU F 102 " 0.014 2.00e-02 2.50e+03 ... (remaining 3119 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4584 2.80 - 3.33: 18099 3.33 - 3.85: 30550 3.85 - 4.38: 36350 4.38 - 4.90: 61927 Nonbonded interactions: 151510 Sorted by model distance: nonbonded pdb=" O LEU A 48 " pdb=" OG1 THR A 51 " model vdw 2.278 3.040 nonbonded pdb=" O LEU B 48 " pdb=" OG1 THR B 51 " model vdw 2.278 3.040 nonbonded pdb=" O LEU E 48 " pdb=" OG1 THR E 51 " model vdw 2.278 3.040 nonbonded pdb=" O LEU D 48 " pdb=" OG1 THR D 51 " model vdw 2.278 3.040 nonbonded pdb=" O LEU F 48 " pdb=" OG1 THR F 51 " model vdw 2.278 3.040 ... (remaining 151505 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 401 or (resid 402 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name C5 or name C6 or name C8 or nam \ e N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or \ name O4 or name O7 or name P1 )) or (resid 403 and (name C1 or name C11 or name \ C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or n \ ame C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C3 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C3 \ 6 or name C37 or name C38 or name C39 or name C5 or name C6 or name C8 or name N \ 1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or nam \ e O4 or name O7 or name P1 )) or (resid 404 and (name C1 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 or na \ me C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 o \ r name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 o \ r name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 \ )) or resid 405)) selection = (chain 'B' and (resid 4 through 401 or (resid 402 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name C5 or name C6 or name C8 or nam \ e N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or \ name O4 or name O7 or name P1 )) or (resid 403 and (name C1 or name C11 or name \ C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or n \ ame C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C3 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C3 \ 6 or name C37 or name C38 or name C39 or name C5 or name C6 or name C8 or name N \ 1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or nam \ e O4 or name O7 or name P1 )) or (resid 404 and (name C1 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 or na \ me C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 o \ r name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 o \ r name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 \ )) or resid 405)) selection = (chain 'C' and (resid 4 through 401 or (resid 402 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name C5 or name C6 or name C8 or nam \ e N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or \ name O4 or name O7 or name P1 )) or (resid 403 and (name C1 or name C11 or name \ C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or n \ ame C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C3 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C3 \ 6 or name C37 or name C38 or name C39 or name C5 or name C6 or name C8 or name N \ 1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or nam \ e O4 or name O7 or name P1 )) or (resid 404 and (name C1 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 or na \ me C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 o \ r name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 o \ r name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 \ )) or resid 405)) selection = (chain 'D' and (resid 4 through 401 or (resid 402 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name C5 or name C6 or name C8 or nam \ e N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or \ name O4 or name O7 or name P1 )) or (resid 403 and (name C1 or name C11 or name \ C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or n \ ame C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C3 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C3 \ 6 or name C37 or name C38 or name C39 or name C5 or name C6 or name C8 or name N \ 1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or nam \ e O4 or name O7 or name P1 )) or (resid 404 and (name C1 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 or na \ me C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 o \ r name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 o \ r name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 \ )) or resid 405)) selection = (chain 'E' and (resid 4 through 401 or (resid 402 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name C5 or name C6 or name C8 or nam \ e N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or \ name O4 or name O7 or name P1 )) or (resid 403 and (name C1 or name C11 or name \ C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or n \ ame C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C3 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C3 \ 6 or name C37 or name C38 or name C39 or name C5 or name C6 or name C8 or name N \ 1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or nam \ e O4 or name O7 or name P1 )) or (resid 404 and (name C1 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 or na \ me C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 o \ r name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 o \ r name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 \ )) or resid 405)) selection = (chain 'F' and (resid 4 through 401 or (resid 402 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name C5 or name C6 or name C8 or nam \ e N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or \ name O4 or name O7 or name P1 )) or (resid 403 and (name C1 or name C11 or name \ C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or n \ ame C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C3 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C3 \ 6 or name C37 or name C38 or name C39 or name C5 or name C6 or name C8 or name N \ 1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or nam \ e O4 or name O7 or name P1 )) or (resid 404 and (name C1 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 or na \ me C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 o \ r name C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 o \ r name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 \ )) or resid 405)) selection = (chain 'G' and (resid 4 through 334 or (resid 401 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C3 or name C30 or name C31 or name C32 or name C33 or name \ C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C5 or n \ ame C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O13 or \ name O14 or name O30 or name O4 or name O7 or name P1 )) or resid 402 through 40 \ 3 or (resid 404 and (name C1 or name C11 or name C12 or name C13 or name C14 or \ name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C20 \ or name C21 or name C3 or name C30 or name C31 or name C32 or name C33 or name C \ 34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C5 or nam \ e C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O13 or na \ me O14 or name O30 or name O4 or name O7 or name P1 )) or (resid 405 and (name C \ 1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or nam \ e C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name C22 or \ name C23 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C5 or name C \ 6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O13 or name \ O14 or name O30 or name O4 or name O7 or name P1 )))) } 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: 4.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 15.810 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0108 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 0.124 19320 Z= 0.230 Angle : 0.754 11.478 25916 Z= 0.357 Chirality : 0.043 0.150 2933 Planarity : 0.003 0.030 3122 Dihedral : 16.864 98.834 7420 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.45 % Allowed : 19.24 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.17), residues: 2303 helix: 2.21 (0.14), residues: 1274 sheet: -0.77 (0.26), residues: 357 loop : -1.97 (0.19), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 271 TYR 0.011 0.001 TYR F 291 PHE 0.009 0.001 PHE D 101 TRP 0.006 0.001 TRP C 184 HIS 0.001 0.000 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00447 (19320) covalent geometry : angle 0.75401 (25914) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.13836 ( 1229) hydrogen bonds : angle 4.74627 ( 3540) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 227 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: -0.0235 (tpp) cc_final: -0.1519 (ptt) REVERT: A 140 MET cc_start: -0.1097 (mmt) cc_final: -0.2680 (mmt) REVERT: B 118 MET cc_start: -0.0370 (tpp) cc_final: -0.1574 (ptt) REVERT: B 140 MET cc_start: -0.1375 (mmt) cc_final: -0.2693 (mmt) REVERT: C 118 MET cc_start: -0.0744 (tpp) cc_final: -0.1687 (ptt) REVERT: C 140 MET cc_start: -0.1531 (mmt) cc_final: -0.2846 (mmt) REVERT: D 118 MET cc_start: -0.0478 (tpp) cc_final: -0.1694 (ptt) REVERT: D 140 MET cc_start: -0.1767 (mmt) cc_final: -0.2948 (mmt) REVERT: E 140 MET cc_start: -0.1546 (mmt) cc_final: -0.2848 (mmt) REVERT: F 118 MET cc_start: -0.0735 (tpp) cc_final: -0.1699 (ptt) REVERT: F 140 MET cc_start: -0.1155 (mmt) cc_final: -0.2564 (mmt) REVERT: G 118 MET cc_start: -0.0274 (tpp) cc_final: -0.1489 (ptt) REVERT: G 140 MET cc_start: -0.1317 (mmt) cc_final: -0.2690 (mmt) outliers start: 8 outliers final: 1 residues processed: 235 average time/residue: 0.5316 time to fit residues: 141.0423 Evaluate side-chains 154 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 220 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.1128 > 50: distance: 49 - 51: 4.505 distance: 51 - 52: 11.329 distance: 52 - 53: 16.426 distance: 52 - 55: 25.565 distance: 53 - 54: 40.504 distance: 53 - 59: 19.213 distance: 55 - 56: 21.401 distance: 56 - 57: 35.049 distance: 56 - 58: 17.483 distance: 59 - 60: 13.088 distance: 60 - 61: 34.131 distance: 60 - 63: 36.743 distance: 61 - 62: 41.517 distance: 61 - 73: 23.699 distance: 63 - 64: 36.494 distance: 64 - 65: 19.256 distance: 64 - 66: 9.953 distance: 65 - 67: 7.170 distance: 66 - 68: 6.710 distance: 66 - 69: 12.360 distance: 67 - 68: 7.931 distance: 68 - 70: 7.806 distance: 69 - 71: 7.796 distance: 70 - 72: 10.338 distance: 71 - 72: 8.713 distance: 73 - 74: 24.411 distance: 73 - 152: 11.330 distance: 74 - 75: 17.264 distance: 74 - 77: 23.772 distance: 75 - 76: 31.302 distance: 75 - 81: 16.097 distance: 76 - 149: 27.160 distance: 77 - 78: 13.268 distance: 77 - 79: 18.012 distance: 78 - 80: 14.135 distance: 81 - 82: 23.268 distance: 82 - 83: 17.046 distance: 82 - 85: 21.254 distance: 83 - 84: 23.350 distance: 83 - 92: 10.535 distance: 85 - 86: 10.319 distance: 86 - 87: 5.398 distance: 87 - 88: 10.727 distance: 88 - 89: 9.255 distance: 89 - 90: 5.631 distance: 89 - 91: 9.302 distance: 92 - 93: 15.147 distance: 93 - 94: 18.806 distance: 93 - 96: 23.467 distance: 94 - 95: 33.306 distance: 94 - 98: 33.278 distance: 96 - 97: 9.536 distance: 98 - 99: 34.830 distance: 98 - 104: 26.663 distance: 99 - 100: 15.345 distance: 99 - 102: 33.494 distance: 100 - 101: 10.437 distance: 100 - 105: 10.997 distance: 102 - 103: 8.545 distance: 103 - 104: 12.475 distance: 105 - 106: 37.573 distance: 106 - 107: 15.351 distance: 106 - 109: 26.687 distance: 107 - 108: 12.945 distance: 107 - 113: 8.473 distance: 109 - 110: 14.201 distance: 110 - 111: 18.030 distance: 110 - 112: 16.782 distance: 113 - 114: 6.275 distance: 114 - 115: 20.374 distance: 114 - 117: 26.442 distance: 115 - 116: 41.511 distance: 115 - 124: 12.081 distance: 117 - 118: 18.418 distance: 118 - 119: 9.619 distance: 119 - 120: 5.135 distance: 120 - 121: 4.528 distance: 121 - 122: 3.429 distance: 121 - 123: 3.898 distance: 124 - 125: 34.544 distance: 125 - 126: 19.656 distance: 125 - 128: 7.278 distance: 126 - 127: 46.063 distance: 126 - 132: 25.705 distance: 128 - 129: 26.377 distance: 129 - 130: 8.519 distance: 129 - 131: 12.871 distance: 132 - 133: 18.953 distance: 133 - 134: 29.203 distance: 133 - 136: 38.323 distance: 134 - 135: 19.237 distance: 134 - 140: 11.102 distance: 136 - 137: 25.495 distance: 136 - 138: 34.198 distance: 137 - 139: 9.532