Starting phenix.real_space_refine on Sat Jul 4 00:32:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ud3_42145/07_2026/8ud3_42145.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ud3_42145/07_2026/8ud3_42145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ud3_42145/07_2026/8ud3_42145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ud3_42145/07_2026/8ud3_42145.map" model { file = "/net/cci-nas-00/data/ceres_data/8ud3_42145/07_2026/8ud3_42145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ud3_42145/07_2026/8ud3_42145.cif" } resolution = 2.67 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= 0.046 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 34 5.49 5 S 60 5.16 5 C 10943 2.51 5 N 2807 2.21 5 O 3400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 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: 17244 Number of models: 1 Model: "" Number of chains: 8 Chain: "F" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "D" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "E" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "B" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "A" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "C" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "G" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 340 Classifications: {'RNA': 17} Modifications used: {'rna3p_pyr': 17} Link IDs: {'rna3p': 16} Chain: "H" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 374 Classifications: {'RNA': 17} Modifications used: {'rna3p_pur': 17} Link IDs: {'rna3p': 16} Residues with excluded nonbonded symmetry interactions: 18 residue: pdb=" N AILE F 27 " occ=0.52 ... (14 atoms not shown) pdb=" CD1BILE F 27 " occ=0.48 residue: pdb=" N AASN F 28 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN F 28 " occ=0.48 residue: pdb=" N AASN F 29 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN F 29 " occ=0.48 residue: pdb=" N AILE D 27 " occ=0.52 ... (14 atoms not shown) pdb=" CD1BILE D 27 " occ=0.48 residue: pdb=" N AASN D 28 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN D 28 " occ=0.48 residue: pdb=" N AASN D 29 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN D 29 " occ=0.48 residue: pdb=" N AILE E 27 " occ=0.52 ... (14 atoms not shown) pdb=" CD1BILE E 27 " occ=0.48 residue: pdb=" N AASN E 28 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN E 28 " occ=0.48 residue: pdb=" N AASN E 29 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN E 29 " occ=0.48 residue: pdb=" N AILE B 27 " occ=0.52 ... (14 atoms not shown) pdb=" CD1BILE B 27 " occ=0.48 residue: pdb=" N AASN B 28 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN B 28 " occ=0.48 residue: pdb=" N AASN B 29 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN B 29 " occ=0.48 ... (remaining 6 not shown) Time building chain proxies: 6.68, per 1000 atoms: 0.39 Number of scatterers: 17244 At special positions: 0 Unit cell: (114.08, 122.36, 133.4, 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 60 16.00 P 34 15.00 O 3400 8.00 N 2807 7.00 C 10943 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 1.3 seconds 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3924 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 47 sheets defined 26.8% alpha, 24.6% beta 15 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'F' and resid 1 through 13 Processing helix chain 'F' and resid 50 through 60 Processing helix chain 'F' and resid 68 through 75 Processing helix chain 'F' and resid 113 through 117 Processing helix chain 'F' and resid 129 through 137 Processing helix chain 'F' and resid 207 through 216 Processing helix chain 'F' and resid 217 through 225 Processing helix chain 'F' and resid 231 through 236 Processing helix chain 'F' and resid 250 through 261 removed outlier: 3.567A pdb=" N GLU F 260 " --> pdb=" O LYS F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 308 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 50 through 60 Processing helix chain 'D' and resid 68 through 75 Processing helix chain 'D' and resid 113 through 117 Processing helix chain 'D' and resid 129 through 137 Processing helix chain 'D' and resid 207 through 216 Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 231 through 236 removed outlier: 3.509A pdb=" N VAL D 236 " --> pdb=" O PHE D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.589A pdb=" N GLU D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 50 through 60 Processing helix chain 'E' and resid 68 through 75 Processing helix chain 'E' and resid 113 through 117 Processing helix chain 'E' and resid 129 through 136 Processing helix chain 'E' and resid 207 through 216 Processing helix chain 'E' and resid 217 through 225 Processing helix chain 'E' and resid 231 through 236 Processing helix chain 'E' and resid 250 through 261 removed outlier: 3.526A pdb=" N GLU E 260 " --> pdb=" O LYS E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 308 Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 50 through 60 Processing helix chain 'B' and resid 68 through 75 Processing helix chain 'B' and resid 113 through 117 Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 207 through 216 Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.550A pdb=" N GLU B 260 " --> pdb=" O LYS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 68 through 75 Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.665A pdb=" N GLU A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 308 Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 50 through 60 Processing helix chain 'C' and resid 68 through 75 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 129 through 136 Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.637A pdb=" N GLU C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 308 Processing sheet with id=AA1, first strand: chain 'F' and resid 24 through 27 removed outlier: 6.567A pdb=" N VAL F 31 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 79 through 80 removed outlier: 7.086A pdb=" N ILE F 79 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N ASP F 124 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LYS F 180 " --> pdb=" O GLN F 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'F' and resid 98 through 99 removed outlier: 8.036A pdb=" N THR F 98 " --> pdb=" O ILE F 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AA6, first strand: chain 'F' and resid 264 through 266 removed outlier: 4.958A pdb=" N ILE F 280 " --> pdb=" O CYS F 290 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N CYS F 290 " --> pdb=" O ILE F 280 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 315 through 322 removed outlier: 7.345A pdb=" N SER F 328 " --> pdb=" O PRO F 343 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N MET F 330 " --> pdb=" O PHE F 341 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE F 341 " --> pdb=" O MET F 330 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP F 332 " --> pdb=" O GLU F 339 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 24 through 27 removed outlier: 6.605A pdb=" N VAL D 31 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 79 through 80 removed outlier: 7.194A pdb=" N ILE D 79 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ASP D 124 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 79 through 80 removed outlier: 7.194A pdb=" N ILE D 79 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ASP D 124 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS D 180 " --> pdb=" O GLN D 187 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 86 through 87 Processing sheet with id=AB3, first strand: chain 'D' and resid 98 through 99 removed outlier: 8.016A pdb=" N THR D 98 " --> pdb=" O ILE D 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 160 through 162 Processing sheet with id=AB5, first strand: chain 'D' and resid 264 through 266 removed outlier: 4.949A pdb=" N ILE D 280 " --> pdb=" O CYS D 290 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N CYS D 290 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 315 through 322 removed outlier: 5.863A pdb=" N LYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL D 338 " --> pdb=" O LYS D 334 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 24 through 27 removed outlier: 6.594A pdb=" N VAL E 31 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.098A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N ASP E 124 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.098A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N ASP E 124 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LYS E 180 " --> pdb=" O GLN E 187 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AC2, first strand: chain 'E' and resid 98 through 99 removed outlier: 8.124A pdb=" N THR E 98 " --> pdb=" O ILE E 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 160 through 162 Processing sheet with id=AC4, first strand: chain 'E' and resid 264 through 266 removed outlier: 4.973A pdb=" N ILE E 280 " --> pdb=" O CYS E 290 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N CYS E 290 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 315 through 322 removed outlier: 7.154A pdb=" N SER E 328 " --> pdb=" O PRO E 343 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N MET E 330 " --> pdb=" O PHE E 341 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE E 341 " --> pdb=" O MET E 330 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP E 332 " --> pdb=" O GLU E 339 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 24 through 27 removed outlier: 6.634A pdb=" N VAL B 31 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.133A pdb=" N ILE B 79 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ASP B 124 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.133A pdb=" N ILE B 79 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ASP B 124 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LYS B 180 " --> pdb=" O GLN B 187 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AD1, first strand: chain 'B' and resid 98 through 99 removed outlier: 8.114A pdb=" N THR B 98 " --> pdb=" O ILE B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AD3, first strand: chain 'B' and resid 264 through 266 removed outlier: 4.935A pdb=" N ILE B 280 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N CYS B 290 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 315 through 322 removed outlier: 7.198A pdb=" N SER B 328 " --> pdb=" O PRO B 343 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N MET B 330 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE B 341 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP B 332 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 24 through 26 removed outlier: 6.651A pdb=" N VAL A 31 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.082A pdb=" N ILE A 79 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ASP A 124 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.082A pdb=" N ILE A 79 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ASP A 124 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS A 180 " --> pdb=" O GLN A 187 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AD9, first strand: chain 'A' and resid 98 through 99 removed outlier: 8.093A pdb=" N THR A 98 " --> pdb=" O ILE A 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AE2, first strand: chain 'A' and resid 264 through 266 removed outlier: 5.000A pdb=" N ILE A 280 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N CYS A 290 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 316 through 322 removed outlier: 3.956A pdb=" N TYR A 342 " --> pdb=" O MET A 330 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 24 through 26 removed outlier: 6.599A pdb=" N VAL C 31 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.129A pdb=" N ILE C 79 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N ASP C 124 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.129A pdb=" N ILE C 79 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N ASP C 124 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LYS C 180 " --> pdb=" O GLN C 187 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AE8, first strand: chain 'C' and resid 98 through 99 removed outlier: 8.042A pdb=" N THR C 98 " --> pdb=" O ILE C 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 160 through 162 Processing sheet with id=AF1, first strand: chain 'C' and resid 264 through 266 removed outlier: 4.792A pdb=" N ILE C 280 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N CYS C 290 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 315 through 322 removed outlier: 7.117A pdb=" N SER C 328 " --> pdb=" O PRO C 343 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N MET C 330 " --> pdb=" O PHE C 341 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE C 341 " --> pdb=" O MET C 330 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP C 332 " --> pdb=" O GLU C 339 " (cutoff:3.500A) 650 hydrogen bonds defined for protein. 1668 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 2.86 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4847 1.33 - 1.45: 2870 1.45 - 1.57: 9796 1.57 - 1.69: 66 1.69 - 1.81: 90 Bond restraints: 17669 Sorted by residual: bond pdb=" CA SER C 261 " pdb=" CB SER C 261 " ideal model delta sigma weight residual 1.526 1.503 0.024 9.30e-03 1.16e+04 6.41e+00 bond pdb=" CA PHE C 263 " pdb=" C PHE C 263 " ideal model delta sigma weight residual 1.524 1.492 0.033 1.35e-02 5.49e+03 5.82e+00 bond pdb=" C SER C 261 " pdb=" O SER C 261 " ideal model delta sigma weight residual 1.241 1.220 0.021 1.05e-02 9.07e+03 4.16e+00 bond pdb=" CA LEU E 345 " pdb=" C LEU E 345 " ideal model delta sigma weight residual 1.523 1.496 0.027 1.34e-02 5.57e+03 4.12e+00 bond pdb=" CA PHE C 263 " pdb=" CB PHE C 263 " ideal model delta sigma weight residual 1.534 1.505 0.029 1.45e-02 4.76e+03 4.05e+00 ... (remaining 17664 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 23860 2.08 - 4.15: 251 4.15 - 6.23: 18 6.23 - 8.31: 3 8.31 - 10.39: 3 Bond angle restraints: 24135 Sorted by residual: angle pdb=" O3' U G 7 " pdb=" C3' U G 7 " pdb=" C2' U G 7 " ideal model delta sigma weight residual 113.70 107.74 5.96 1.50e+00 4.44e-01 1.58e+01 angle pdb=" C SER C 261 " pdb=" CA SER C 261 " pdb=" CB SER C 261 " ideal model delta sigma weight residual 110.98 106.39 4.59 1.18e+00 7.18e-01 1.52e+01 angle pdb=" N PRO C 262 " pdb=" CA PRO C 262 " pdb=" C PRO C 262 " ideal model delta sigma weight residual 111.14 116.25 -5.11 1.56e+00 4.11e-01 1.07e+01 angle pdb=" CA LEU D 345 " pdb=" CB LEU D 345 " pdb=" CG LEU D 345 " ideal model delta sigma weight residual 116.30 126.69 -10.39 3.50e+00 8.16e-02 8.80e+00 angle pdb=" O3' U G 15 " pdb=" C3' U G 15 " pdb=" C2' U G 15 " ideal model delta sigma weight residual 113.70 109.27 4.43 1.50e+00 4.44e-01 8.71e+00 ... (remaining 24130 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.09: 9382 21.09 - 42.18: 875 42.18 - 63.27: 259 63.27 - 84.36: 38 84.36 - 105.45: 20 Dihedral angle restraints: 10574 sinusoidal: 4490 harmonic: 6084 Sorted by residual: dihedral pdb=" CA THR A 192 " pdb=" C THR A 192 " pdb=" N TYR A 193 " pdb=" CA TYR A 193 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA THR D 192 " pdb=" C THR D 192 " pdb=" N TYR D 193 " pdb=" CA TYR D 193 " ideal model delta harmonic sigma weight residual 180.00 160.53 19.47 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA THR E 192 " pdb=" C THR E 192 " pdb=" N TYR E 193 " pdb=" CA TYR E 193 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 10571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2068 0.046 - 0.092: 471 0.092 - 0.138: 217 0.138 - 0.184: 39 0.184 - 0.230: 9 Chirality restraints: 2804 Sorted by residual: chirality pdb=" C3' U G 15 " pdb=" C4' U G 15 " pdb=" O3' U G 15 " pdb=" C2' U G 15 " both_signs ideal model delta sigma weight residual False -2.48 -2.71 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C3' U G 7 " pdb=" C4' U G 7 " pdb=" O3' U G 7 " pdb=" C2' U G 7 " both_signs ideal model delta sigma weight residual False -2.48 -2.70 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C2' A H 1 " pdb=" C3' A H 1 " pdb=" O2' A H 1 " pdb=" C1' A H 1 " both_signs ideal model delta sigma weight residual False -2.75 -2.56 -0.19 2.00e-01 2.50e+01 9.43e-01 ... (remaining 2801 not shown) Planarity restraints: 2986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 204 " 0.050 5.00e-02 4.00e+02 7.57e-02 9.16e+00 pdb=" N PRO F 205 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO F 205 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 205 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 269 " -0.028 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO B 270 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 345 " 0.007 2.00e-02 2.50e+03 1.50e-02 2.24e+00 pdb=" C LEU F 345 " -0.026 2.00e-02 2.50e+03 pdb=" O LEU F 345 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN F 346 " 0.009 2.00e-02 2.50e+03 ... (remaining 2983 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2005 2.75 - 3.29: 16400 3.29 - 3.83: 30887 3.83 - 4.36: 38106 4.36 - 4.90: 63296 Nonbonded interactions: 150694 Sorted by model distance: nonbonded pdb=" OH TYR A 193 " pdb=" OE2 GLU A 304 " model vdw 2.217 3.040 nonbonded pdb=" O HIS D 242 " pdb=" OG SER D 287 " model vdw 2.223 3.040 nonbonded pdb=" O HIS E 242 " pdb=" OG SER E 287 " model vdw 2.245 3.040 nonbonded pdb=" O HIS C 242 " pdb=" OG SER C 287 " model vdw 2.245 3.040 nonbonded pdb=" NH1 ARG E 198 " pdb=" OE1 GLU E 210 " model vdw 2.251 3.120 ... (remaining 150689 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 1 through 26 or resid 30 through 346)) selection = (chain 'B' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'C' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'D' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'E' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'F' and (resid 1 through 26 or resid 30 through 346)) } 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=0.48 max=1.00 mean=0.99 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.000 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.590 Find NCS groups from input model: 0.320 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:8.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 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 : 0.003 0.055 17669 Z= 0.151 Angle : 0.529 10.385 24135 Z= 0.305 Chirality : 0.050 0.230 2804 Planarity : 0.003 0.076 2986 Dihedral : 18.218 105.447 6650 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.65 % Allowed : 23.92 % Favored : 75.43 % 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: 0.47 (0.19), residues: 2094 helix: 0.52 (0.23), residues: 534 sheet: 0.53 (0.28), residues: 342 loop : 0.27 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 135 TYR 0.008 0.001 TYR F 342 PHE 0.018 0.001 PHE D 258 TRP 0.018 0.001 TRP A 332 HIS 0.013 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (17669) covalent geometry : angle 0.52900 / 0.30 (24135) hydrogen bonds : bond 0.18610 / 12.04 ( 635) hydrogen bonds : angle 8.37318 / 6.01 ( 1728) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 0.495 Fit side-chains REVERT: E 16 ASP cc_start: 0.8143 (t0) cc_final: 0.7497 (t70) REVERT: E 188 GLN cc_start: 0.7816 (tp40) cc_final: 0.7324 (tm-30) REVERT: B 266 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7458 (tt0) REVERT: A 345 LEU cc_start: 0.5690 (OUTLIER) cc_final: 0.5008 (tt) REVERT: C 191 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7769 (mm-30) outliers start: 12 outliers final: 3 residues processed: 201 average time/residue: 0.5576 time to fit residues: 125.3670 Evaluate side-chains 182 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 177 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 328 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 HIS C 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.165237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.112055 restraints weight = 107070.279| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.95 r_work: 0.2798 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17669 Z= 0.226 Angle : 0.569 9.423 24135 Z= 0.306 Chirality : 0.050 0.198 2804 Planarity : 0.004 0.062 2986 Dihedral : 10.703 84.425 2693 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.80 % Allowed : 22.04 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.19), residues: 2094 helix: 0.32 (0.22), residues: 540 sheet: 0.56 (0.28), residues: 354 loop : 0.25 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 126 TYR 0.015 0.002 TYR E 225 PHE 0.016 0.002 PHE B 15 TRP 0.011 0.002 TRP A 332 HIS 0.012 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.23 (17669) covalent geometry : angle 0.56912 / 0.31 (24135) hydrogen bonds : bond 0.05395 / 3.60 ( 635) hydrogen bonds : angle 6.29422 / 4.50 ( 1728) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 188 time to evaluate : 0.757 Fit side-chains REVERT: F 187 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7580 (mt0) REVERT: F 224 ARG cc_start: 0.7399 (ttm170) cc_final: 0.6817 (ttm-80) REVERT: F 228 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6709 (mp0) REVERT: D 21 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7606 (mt-10) REVERT: E 21 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: E 220 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.6140 (mp0) REVERT: E 264 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7463 (mm-30) REVERT: B 345 LEU cc_start: 0.6034 (OUTLIER) cc_final: 0.5812 (pp) REVERT: A 328 SER cc_start: 0.8833 (p) cc_final: 0.8587 (m) REVERT: A 345 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.5769 (tp) REVERT: C 191 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8061 (mm-30) outliers start: 50 outliers final: 12 residues processed: 219 average time/residue: 0.6497 time to fit residues: 158.2485 Evaluate side-chains 200 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 147 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 80 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 chunk 135 optimal weight: 7.9990 chunk 204 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 198 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 346 GLN A 337 HIS C 14 HIS C 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.165710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.112207 restraints weight = 104859.994| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.80 r_work: 0.2816 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17669 Z= 0.133 Angle : 0.496 8.906 24135 Z= 0.266 Chirality : 0.046 0.164 2804 Planarity : 0.004 0.051 2986 Dihedral : 10.142 83.426 2687 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.37 % Allowed : 22.31 % Favored : 75.32 % 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: 0.42 (0.19), residues: 2094 helix: 0.49 (0.23), residues: 540 sheet: 0.61 (0.28), residues: 354 loop : 0.20 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 138 TYR 0.010 0.001 TYR E 225 PHE 0.013 0.001 PHE E 240 TRP 0.011 0.001 TRP A 332 HIS 0.010 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (17669) covalent geometry : angle 0.49568 / 0.27 (24135) hydrogen bonds : bond 0.04351 / 2.89 ( 635) hydrogen bonds : angle 5.78681 / 4.15 ( 1728) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 191 time to evaluate : 0.632 Fit side-chains REVERT: F 21 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: F 103 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8441 (p) REVERT: F 187 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7535 (mt0) REVERT: F 339 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7323 (pt0) REVERT: D 21 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7602 (mt-10) REVERT: D 232 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.7104 (m-80) REVERT: D 254 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6942 (tp) REVERT: E 220 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.6079 (mp0) REVERT: E 241 SER cc_start: 0.8819 (m) cc_final: 0.8618 (m) REVERT: E 264 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7386 (mm-30) REVERT: E 346 GLN cc_start: 0.4677 (OUTLIER) cc_final: 0.4415 (tp40) REVERT: B 218 MET cc_start: 0.7342 (ttp) cc_final: 0.7098 (ttm) REVERT: B 264 GLU cc_start: 0.6847 (tm-30) cc_final: 0.6548 (tm-30) REVERT: B 266 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7554 (tt0) REVERT: B 345 LEU cc_start: 0.6068 (OUTLIER) cc_final: 0.5842 (pp) REVERT: A 284 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7270 (tm-30) REVERT: A 345 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.5661 (tt) REVERT: C 12 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8059 (mttt) REVERT: C 191 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7891 (mm-30) outliers start: 42 outliers final: 9 residues processed: 223 average time/residue: 0.5906 time to fit residues: 147.7716 Evaluate side-chains 198 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 339 GLU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 12 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 183 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 120 optimal weight: 0.0980 chunk 28 optimal weight: 4.9990 chunk 197 optimal weight: 0.9980 chunk 176 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 163 ASN D 277 ASN E 346 GLN A 337 HIS C 163 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.167149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.127975 restraints weight = 100623.465| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 5.70 r_work: 0.2743 rms_B_bonded: 5.10 restraints_weight: 2.0000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17669 Z= 0.175 Angle : 0.518 9.818 24135 Z= 0.277 Chirality : 0.047 0.186 2804 Planarity : 0.004 0.046 2986 Dihedral : 9.980 82.639 2686 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.80 % Allowed : 22.04 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.19), residues: 2094 helix: 0.47 (0.23), residues: 540 sheet: 0.64 (0.28), residues: 354 loop : 0.19 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 138 TYR 0.011 0.001 TYR E 225 PHE 0.013 0.002 PHE C 329 TRP 0.006 0.001 TRP B 332 HIS 0.010 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (17669) covalent geometry : angle 0.51792 / 0.28 (24135) hydrogen bonds : bond 0.04277 / 2.85 ( 635) hydrogen bonds : angle 5.72983 / 4.09 ( 1728) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 0.646 Fit side-chains REVERT: F 21 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8246 (mt-10) REVERT: F 103 SER cc_start: 0.8833 (OUTLIER) cc_final: 0.8480 (p) REVERT: F 187 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7634 (mt0) REVERT: F 204 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7168 (mmtm) REVERT: F 224 ARG cc_start: 0.7378 (ttm170) cc_final: 0.6824 (ttm-80) REVERT: F 339 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7338 (pt0) REVERT: D 21 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7701 (mt-10) REVERT: D 232 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.7101 (m-80) REVERT: D 245 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7292 (tt) REVERT: D 254 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.7008 (tp) REVERT: E 21 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8033 (mt-10) REVERT: E 241 SER cc_start: 0.8803 (m) cc_final: 0.8601 (m) REVERT: E 264 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7377 (mm-30) REVERT: B 264 GLU cc_start: 0.6893 (tm-30) cc_final: 0.6606 (tm-30) REVERT: B 266 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7612 (tt0) REVERT: B 344 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6673 (tmtt) REVERT: B 345 LEU cc_start: 0.6067 (OUTLIER) cc_final: 0.5704 (pp) REVERT: A 232 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.6972 (t80) REVERT: A 264 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7641 (mt-10) REVERT: A 284 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7255 (tm-30) REVERT: A 345 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.5756 (tt) REVERT: A 346 GLN cc_start: 0.5710 (OUTLIER) cc_final: 0.4516 (tm-30) REVERT: C 12 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8092 (mttt) REVERT: C 152 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.6914 (pm20) REVERT: C 191 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7948 (mm-30) outliers start: 50 outliers final: 17 residues processed: 209 average time/residue: 0.5956 time to fit residues: 139.5779 Evaluate side-chains 212 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 204 LYS Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 339 GLU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 152 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 61 optimal weight: 0.0970 chunk 133 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.165947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.112695 restraints weight = 101470.957| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.91 r_work: 0.2801 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17669 Z= 0.219 Angle : 0.549 10.091 24135 Z= 0.292 Chirality : 0.049 0.192 2804 Planarity : 0.004 0.055 2986 Dihedral : 9.808 81.732 2686 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.12 % Allowed : 22.20 % Favored : 74.68 % 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: 0.31 (0.19), residues: 2094 helix: 0.42 (0.23), residues: 534 sheet: 0.67 (0.28), residues: 354 loop : 0.07 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 138 TYR 0.013 0.002 TYR E 225 PHE 0.017 0.002 PHE C 329 TRP 0.007 0.001 TRP B 332 HIS 0.004 0.001 HIS F 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.22 (17669) covalent geometry : angle 0.54861 / 0.29 (24135) hydrogen bonds : bond 0.04467 / 2.98 ( 635) hydrogen bonds : angle 5.75697 / 4.10 ( 1728) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 178 time to evaluate : 0.609 Fit side-chains REVERT: F 21 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8166 (mt-10) REVERT: F 34 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8455 (ttpp) REVERT: F 103 SER cc_start: 0.8857 (OUTLIER) cc_final: 0.8504 (p) REVERT: F 187 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7585 (mt0) REVERT: F 204 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7230 (mmtm) REVERT: F 224 ARG cc_start: 0.7436 (ttm170) cc_final: 0.7197 (ttm-80) REVERT: F 277 ASN cc_start: 0.8892 (m-40) cc_final: 0.8640 (m-40) REVERT: D 21 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: D 232 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.7142 (m-80) REVERT: D 245 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7380 (tt) REVERT: D 254 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.7021 (tp) REVERT: D 284 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7405 (tt0) REVERT: E 21 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: E 264 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7391 (mm-30) REVERT: B 264 GLU cc_start: 0.6884 (tm-30) cc_final: 0.6606 (tm-30) REVERT: B 266 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7630 (tt0) REVERT: B 344 LYS cc_start: 0.7005 (OUTLIER) cc_final: 0.6720 (tmtt) REVERT: B 345 LEU cc_start: 0.5985 (OUTLIER) cc_final: 0.5627 (pp) REVERT: A 264 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7625 (mt-10) REVERT: A 284 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7189 (tm-30) REVERT: A 345 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.5852 (tt) REVERT: A 346 GLN cc_start: 0.5844 (OUTLIER) cc_final: 0.4613 (tm-30) REVERT: C 12 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8074 (mttt) REVERT: C 191 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7892 (mm-30) outliers start: 54 outliers final: 20 residues processed: 217 average time/residue: 0.5261 time to fit residues: 127.9008 Evaluate side-chains 214 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 204 LYS Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 284 GLN Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 147 SER 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: 53.6432 > 50: distance: 48 - 157: 9.507 distance: 51 - 154: 8.989 distance: 76 - 82: 14.408 distance: 82 - 83: 17.951 distance: 82 - 88: 27.623 distance: 83 - 84: 23.326 distance: 83 - 86: 21.719 distance: 84 - 85: 15.610 distance: 84 - 89: 11.767 distance: 86 - 87: 24.505 distance: 87 - 88: 17.211 distance: 89 - 90: 24.607 distance: 90 - 91: 9.771 distance: 90 - 93: 18.341 distance: 91 - 92: 25.641 distance: 91 - 97: 16.784 distance: 93 - 94: 19.254 distance: 94 - 95: 7.916 distance: 95 - 96: 19.962 distance: 97 - 98: 9.912 distance: 98 - 99: 10.787 distance: 98 - 101: 16.187 distance: 99 - 100: 36.573 distance: 99 - 105: 18.903 distance: 101 - 102: 15.426 distance: 102 - 103: 40.388 distance: 102 - 104: 14.780 distance: 105 - 106: 17.888 distance: 106 - 107: 10.368 distance: 106 - 109: 24.927 distance: 107 - 108: 11.842 distance: 107 - 111: 11.658 distance: 109 - 110: 17.460 distance: 111 - 112: 18.476 distance: 112 - 113: 11.646 distance: 112 - 115: 12.930 distance: 113 - 114: 20.878 distance: 113 - 118: 15.746 distance: 115 - 116: 6.118 distance: 115 - 117: 29.353 distance: 118 - 119: 18.804 distance: 119 - 120: 9.998 distance: 119 - 122: 10.432 distance: 120 - 121: 23.798 distance: 120 - 125: 12.086 distance: 122 - 123: 8.330 distance: 122 - 124: 17.054 distance: 125 - 126: 15.648 distance: 125 - 204: 17.030 distance: 126 - 127: 12.457 distance: 126 - 129: 5.020 distance: 127 - 128: 16.783 distance: 127 - 134: 3.118 distance: 128 - 201: 15.996 distance: 129 - 130: 15.633 distance: 130 - 131: 5.633 distance: 131 - 132: 16.334 distance: 132 - 133: 14.572 distance: 134 - 135: 6.770 distance: 135 - 136: 20.875 distance: 135 - 138: 13.369 distance: 136 - 137: 13.420 distance: 136 - 142: 19.234 distance: 138 - 139: 14.009 distance: 139 - 140: 15.187 distance: 139 - 141: 22.166 distance: 142 - 143: 5.064 distance: 142 - 193: 10.068 distance: 143 - 146: 11.295 distance: 144 - 145: 10.602 distance: 144 - 154: 6.325 distance: 145 - 190: 11.450 distance: 147 - 148: 10.561 distance: 147 - 149: 9.713 distance: 148 - 150: 5.699 distance: 149 - 151: 10.665 distance: 150 - 152: 5.879 distance: 151 - 152: 10.890 distance: 152 - 153: 19.379 distance: 154 - 155: 7.664 distance: 155 - 158: 6.610 distance: 156 - 157: 5.556 distance: 156 - 165: 6.778 distance: 158 - 159: 7.651 distance: 159 - 160: 5.740 distance: 159 - 161: 6.313 distance: 160 - 162: 12.082 distance: 161 - 163: 13.333 distance: 162 - 164: 10.376 distance: 163 - 164: 11.492