Starting phenix.real_space_refine on Thu Aug 6 22:07:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ud5_42147/08_2026/8ud5_42147.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ud5_42147/08_2026/8ud5_42147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ud5_42147/08_2026/8ud5_42147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ud5_42147/08_2026/8ud5_42147.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ud5_42147/08_2026/8ud5_42147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ud5_42147/08_2026/8ud5_42147.map" } resolution = 3.13 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= 0.042 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 53 5.49 5 S 60 5.16 5 C 11133 2.51 5 N 2880 2.21 5 O 3538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17664 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: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 542 Classifications: {'RNA': 27} Modifications used: {'5*END': 1, 'rna3p_pur': 2, 'rna3p_pyr': 25} Link IDs: {'rna3p': 26} Chain: "H" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 592 Classifications: {'RNA': 27} Modifications used: {'rna3p_pur': 25, 'rna3p_pyr': 2} Link IDs: {'rna3p': 26} 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: 6.54, per 1000 atoms: 0.37 Number of scatterers: 17664 At special positions: 0 Unit cell: (115.92, 118.68, 129.72, 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 53 15.00 O 3538 8.00 N 2880 7.00 C 11133 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: 1.33 Conformation dependent library (CDL) restraints added in 1.2 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: 58 helices and 46 sheets defined 26.3% alpha, 24.0% beta 20 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 2.05 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 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 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 Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.744A 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 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 removed outlier: 3.928A pdb=" N VAL E 236 " --> pdb=" O PHE E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 261 removed outlier: 3.766A 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 removed outlier: 3.531A pdb=" N VAL B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.580A 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 removed outlier: 3.520A pdb=" N VAL A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.649A 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 removed outlier: 3.624A pdb=" N VAL C 236 " --> pdb=" O PHE C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.631A 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: 6.632A 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: 7.268A pdb=" N ILE F 79 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ASP F 124 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 4.716A 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: 8.208A 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: 3.536A pdb=" N GLU F 266 " --> pdb=" O PHE F 279 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE F 280 " --> pdb=" O CYS F 290 " (cutoff:3.500A) removed outlier: 5.309A 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: 7.357A pdb=" N SER F 328 " --> pdb=" O PRO F 343 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N MET F 330 " --> pdb=" O PHE F 341 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE F 341 " --> pdb=" O MET F 330 " (cutoff:3.500A) removed outlier: 6.421A 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: 6.684A 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: 7.190A pdb=" N ILE D 79 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N ASP D 124 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LYS D 180 " --> pdb=" O GLN D 187 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 86 through 87 Processing sheet with id=AB2, first strand: chain 'D' and resid 98 through 99 removed outlier: 8.236A pdb=" N THR D 98 " --> pdb=" O ILE D 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 160 through 162 Processing sheet with id=AB4, first strand: chain 'D' and resid 264 through 266 removed outlier: 4.869A pdb=" N ILE D 280 " --> pdb=" O CYS D 290 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N CYS D 290 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 315 through 322 removed outlier: 5.879A pdb=" N LYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL D 338 " --> pdb=" O LYS D 334 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 24 through 27 removed outlier: 6.658A pdb=" N VAL E 31 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.176A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N ASP E 124 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.176A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N ASP E 124 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LYS E 180 " --> pdb=" O GLN E 187 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AC1, first strand: chain 'E' and resid 98 through 99 removed outlier: 8.306A pdb=" N THR E 98 " --> pdb=" O ILE E 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 160 through 162 Processing sheet with id=AC3, first strand: chain 'E' and resid 275 through 281 removed outlier: 4.915A pdb=" N ILE E 280 " --> pdb=" O CYS E 290 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N CYS E 290 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 315 through 322 removed outlier: 7.151A pdb=" N SER E 328 " --> pdb=" O PRO E 343 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N MET E 330 " --> pdb=" O PHE E 341 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE E 341 " --> pdb=" O MET E 330 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP E 332 " --> pdb=" O GLU E 339 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 24 through 27 removed outlier: 6.698A pdb=" N VAL B 31 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.220A pdb=" N ILE B 79 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N ASP B 124 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.220A pdb=" N ILE B 79 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N ASP B 124 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LYS B 180 " --> pdb=" O GLN B 187 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AC9, first strand: chain 'B' and resid 98 through 99 removed outlier: 8.108A pdb=" N THR B 98 " --> pdb=" O ILE B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AD2, first strand: chain 'B' and resid 264 through 266 removed outlier: 5.005A pdb=" N ILE B 280 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N CYS B 290 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 315 through 322 removed outlier: 6.677A pdb=" N TRP B 332 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 24 through 26 removed outlier: 6.685A pdb=" N VAL A 31 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.190A pdb=" N ILE A 79 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ASP A 124 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.190A pdb=" N ILE A 79 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ASP A 124 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS A 180 " --> pdb=" O GLN A 187 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AD8, first strand: chain 'A' and resid 98 through 99 removed outlier: 8.202A pdb=" N THR A 98 " --> pdb=" O ILE A 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AE1, first strand: chain 'A' and resid 264 through 266 removed outlier: 5.093A pdb=" N ILE A 280 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N CYS A 290 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 316 through 322 removed outlier: 7.255A pdb=" N SER A 328 " --> pdb=" O PRO A 343 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET A 330 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE A 341 " --> pdb=" O MET A 330 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TRP A 332 " --> pdb=" O GLU A 339 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 24 through 26 removed outlier: 6.634A pdb=" N VAL C 31 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.144A pdb=" N ILE C 79 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ASP C 124 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.144A pdb=" N ILE C 79 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ASP C 124 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LYS C 180 " --> pdb=" O GLN C 187 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AE7, first strand: chain 'C' and resid 98 through 99 removed outlier: 8.168A pdb=" N THR C 98 " --> pdb=" O ILE C 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 160 through 162 Processing sheet with id=AE9, first strand: chain 'C' and resid 264 through 266 removed outlier: 4.683A pdb=" N ILE C 280 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N CYS C 290 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 315 through 322 removed outlier: 3.547A pdb=" N THR C 340 " --> pdb=" O TRP C 332 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N VAL C 338 " --> pdb=" O LYS C 334 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1632 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 3.27 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5443 1.34 - 1.45: 2718 1.45 - 1.57: 9783 1.57 - 1.69: 105 1.69 - 1.81: 90 Bond restraints: 18139 Sorted by residual: bond pdb=" CA LEU B 345 " pdb=" C LEU B 345 " ideal model delta sigma weight residual 1.526 1.496 0.030 1.29e-02 6.01e+03 5.49e+00 bond pdb=" C1' G G 21 " pdb=" N9 G G 21 " ideal model delta sigma weight residual 1.483 1.457 0.026 1.50e-02 4.44e+03 2.94e+00 bond pdb=" C1' A G 24 " pdb=" N9 A G 24 " ideal model delta sigma weight residual 1.483 1.459 0.024 1.50e-02 4.44e+03 2.47e+00 bond pdb=" O3' U G 4 " pdb=" P U G 5 " ideal model delta sigma weight residual 1.607 1.589 0.018 1.20e-02 6.94e+03 2.37e+00 bond pdb=" C1' A H 29 " pdb=" N9 A H 29 " ideal model delta sigma weight residual 1.483 1.461 0.022 1.50e-02 4.44e+03 2.16e+00 ... (remaining 18134 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 24535 1.91 - 3.81: 306 3.81 - 5.72: 21 5.72 - 7.63: 4 7.63 - 9.53: 1 Bond angle restraints: 24867 Sorted by residual: angle pdb=" N LYS B 344 " pdb=" CA LYS B 344 " pdb=" C LYS B 344 " ideal model delta sigma weight residual 110.24 116.81 -6.57 1.30e+00 5.92e-01 2.55e+01 angle pdb=" C LYS C 344 " pdb=" N LEU C 345 " pdb=" CA LEU C 345 " ideal model delta sigma weight residual 121.54 128.71 -7.17 1.91e+00 2.74e-01 1.41e+01 angle pdb=" CA PRO A 262 " pdb=" N PRO A 262 " pdb=" CD PRO A 262 " ideal model delta sigma weight residual 112.00 107.30 4.70 1.40e+00 5.10e-01 1.13e+01 angle pdb=" O5' C G 27 " pdb=" C5' C G 27 " pdb=" C4' C G 27 " ideal model delta sigma weight residual 109.40 111.94 -2.54 8.00e-01 1.56e+00 1.01e+01 angle pdb=" O5' U G 19 " pdb=" C5' U G 19 " pdb=" C4' U G 19 " ideal model delta sigma weight residual 109.40 111.91 -2.51 8.00e-01 1.56e+00 9.84e+00 ... (remaining 24862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.40: 9478 19.40 - 38.80: 991 38.80 - 58.20: 301 58.20 - 77.60: 74 77.60 - 96.99: 25 Dihedral angle restraints: 10869 sinusoidal: 4785 harmonic: 6084 Sorted by residual: dihedral pdb=" C3' A H 27 " pdb=" C4' A H 27 " pdb=" O4' A H 27 " pdb=" C1' A H 27 " ideal model delta sinusoidal sigma weight residual 20.00 -10.12 30.12 1 8.00e+00 1.56e-02 2.03e+01 dihedral pdb=" C4' A H 27 " pdb=" O4' A H 27 " pdb=" C1' A H 27 " pdb=" C2' A H 27 " ideal model delta sinusoidal sigma weight residual 3.00 29.51 -26.51 1 8.00e+00 1.56e-02 1.58e+01 dihedral pdb=" C5' A H 27 " pdb=" C4' A H 27 " pdb=" C3' A H 27 " pdb=" O3' A H 27 " ideal model delta sinusoidal sigma weight residual 82.00 108.06 -26.06 1 8.00e+00 1.56e-02 1.53e+01 ... (remaining 10866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2236 0.047 - 0.095: 431 0.095 - 0.142: 224 0.142 - 0.190: 7 0.190 - 0.237: 5 Chirality restraints: 2903 Sorted by residual: chirality pdb=" C3' A G 24 " pdb=" C4' A G 24 " pdb=" O3' A G 24 " pdb=" C2' A G 24 " both_signs ideal model delta sigma weight residual False -2.48 -2.71 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C3' A H 29 " pdb=" C4' A H 29 " pdb=" O3' A H 29 " pdb=" C2' A H 29 " both_signs ideal model delta sigma weight residual False -2.48 -2.71 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C3' A H 26 " pdb=" C4' A H 26 " pdb=" O3' A H 26 " pdb=" C2' A H 26 " both_signs ideal model delta sigma weight residual False -2.48 -2.69 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2900 not shown) Planarity restraints: 3006 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 261 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO A 262 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO A 262 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 262 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 261 " 0.066 5.00e-02 4.00e+02 9.89e-02 1.57e+01 pdb=" N PRO D 262 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO D 262 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO D 262 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 204 " 0.034 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO F 205 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO F 205 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 205 " 0.029 5.00e-02 4.00e+02 ... (remaining 3003 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2934 2.77 - 3.30: 16539 3.30 - 3.84: 30684 3.84 - 4.37: 37739 4.37 - 4.90: 63421 Nonbonded interactions: 151317 Sorted by model distance: nonbonded pdb=" O HIS A 242 " pdb=" OG SER A 287 " model vdw 2.238 3.040 nonbonded pdb=" O HIS E 242 " pdb=" OG SER E 287 " model vdw 2.240 3.040 nonbonded pdb=" OG1 THR B 195 " pdb=" OD2 ASP B 323 " model vdw 2.271 3.040 nonbonded pdb=" OH TYR A 193 " pdb=" OE2 GLU A 304 " model vdw 2.281 3.040 nonbonded pdb=" O HIS D 242 " pdb=" OG SER D 287 " model vdw 2.293 3.040 ... (remaining 151312 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.190 Find NCS groups from input model: 0.370 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 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 : 0.002 0.072 18139 Z= 0.127 Angle : 0.502 9.534 24867 Z= 0.310 Chirality : 0.047 0.237 2903 Planarity : 0.004 0.110 3006 Dihedral : 18.013 96.995 6945 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.27 % Allowed : 22.10 % Favored : 77.63 % 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: 0.54 (0.19), residues: 2094 helix: 0.73 (0.23), residues: 534 sheet: 0.54 (0.30), residues: 342 loop : 0.26 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 135 TYR 0.009 0.001 TYR A 342 PHE 0.027 0.001 PHE D 258 TRP 0.014 0.001 TRP B 332 HIS 0.003 0.001 HIS B 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.13 (18139) covalent geometry : angle 0.50183 / 0.31 (24867) hydrogen bonds : bond 0.20642 / 13.83 ( 637) hydrogen bonds : angle 8.36966 / 5.97 ( 1718) *********************** 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 220 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 215 time to evaluate : 0.491 Fit side-chains REVERT: F 56 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8055 (mp0) REVERT: B 223 GLU cc_start: 0.8180 (tp30) cc_final: 0.7712 (tt0) REVERT: A 202 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7388 (tt0) outliers start: 5 outliers final: 2 residues processed: 219 average time/residue: 0.1324 time to fit residues: 44.9080 Evaluate side-chains 207 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 204 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 136 ASN Chi-restraints excluded: chain A residue 197 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 0.0370 chunk 122 optimal weight: 0.0070 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 GLN B 277 ASN A 199 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.165165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.121129 restraints weight = 112214.254| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 5.06 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.0748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18139 Z= 0.125 Angle : 0.503 9.905 24867 Z= 0.278 Chirality : 0.045 0.148 2903 Planarity : 0.005 0.088 3006 Dihedral : 12.163 90.988 2985 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.61 % Allowed : 21.34 % Favored : 77.04 % 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: 0.54 (0.19), residues: 2094 helix: 0.73 (0.23), residues: 540 sheet: 0.53 (0.29), residues: 342 loop : 0.25 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 224 TYR 0.010 0.001 TYR C 179 PHE 0.011 0.001 PHE D 329 TRP 0.006 0.001 TRP B 86 HIS 0.003 0.001 HIS B 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (18139) covalent geometry : angle 0.50346 / 0.28 (24867) hydrogen bonds : bond 0.05014 / 3.31 ( 637) hydrogen bonds : angle 6.10619 / 4.35 ( 1718) *********************** 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 248 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 0.650 Fit side-chains REVERT: F 56 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: F 264 GLU cc_start: 0.7344 (mp0) cc_final: 0.7060 (mt-10) REVERT: D 104 MET cc_start: 0.8636 (mmm) cc_final: 0.8085 (tpt) REVERT: D 152 GLN cc_start: 0.7659 (pm20) cc_final: 0.7421 (mm-40) REVERT: E 233 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6670 (mm-30) outliers start: 29 outliers final: 18 residues processed: 232 average time/residue: 0.1429 time to fit residues: 50.7990 Evaluate side-chains 227 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 208 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 77 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 chunk 177 optimal weight: 1.9990 chunk 205 optimal weight: 30.0000 chunk 32 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 GLN B 74 ASN B 175 GLN C 187 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.161105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.117719 restraints weight = 109911.682| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 5.31 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18139 Z= 0.198 Angle : 0.528 9.255 24867 Z= 0.285 Chirality : 0.047 0.147 2903 Planarity : 0.004 0.079 3006 Dihedral : 12.044 90.007 2983 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.10 % Allowed : 20.70 % Favored : 77.20 % 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: 0.30 (0.19), residues: 2094 helix: 0.46 (0.23), residues: 546 sheet: 0.52 (0.29), residues: 342 loop : 0.09 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 224 TYR 0.018 0.002 TYR A 225 PHE 0.015 0.002 PHE F 329 TRP 0.008 0.001 TRP A 332 HIS 0.004 0.001 HIS C 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 (18139) covalent geometry : angle 0.52835 / 0.28 (24867) hydrogen bonds : bond 0.04668 / 3.12 ( 637) hydrogen bonds : angle 5.79762 / 4.14 ( 1718) *********************** 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 245 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 210 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: D 104 MET cc_start: 0.8760 (mmm) cc_final: 0.8269 (tpt) REVERT: D 264 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: B 104 MET cc_start: 0.8656 (mmm) cc_final: 0.8365 (tpt) REVERT: A 163 ASN cc_start: 0.8172 (t0) cc_final: 0.7951 (t0) REVERT: A 170 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7733 (mt-10) REVERT: A 345 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6508 (tp) REVERT: C 264 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6587 (mt-10) outliers start: 35 outliers final: 21 residues processed: 224 average time/residue: 0.1462 time to fit residues: 49.9006 Evaluate side-chains 230 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 63 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.162200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.118512 restraints weight = 108899.148| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 5.28 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18139 Z= 0.152 Angle : 0.500 8.754 24867 Z= 0.268 Chirality : 0.045 0.144 2903 Planarity : 0.004 0.073 3006 Dihedral : 11.923 90.385 2983 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.83 % Allowed : 21.08 % Favored : 77.10 % 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: 0.30 (0.19), residues: 2094 helix: 0.55 (0.23), residues: 540 sheet: 0.55 (0.29), residues: 342 loop : 0.03 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 224 TYR 0.013 0.001 TYR A 225 PHE 0.012 0.001 PHE F 134 TRP 0.007 0.001 TRP B 86 HIS 0.003 0.001 HIS B 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (18139) covalent geometry : angle 0.50042 / 0.27 (24867) hydrogen bonds : bond 0.04056 / 2.70 ( 637) hydrogen bonds : angle 5.55539 / 3.97 ( 1718) *********************** 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 240 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: D 104 MET cc_start: 0.8754 (mmm) cc_final: 0.8268 (tpt) REVERT: D 264 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7232 (tt0) REVERT: B 104 MET cc_start: 0.8660 (mmm) cc_final: 0.8361 (tpt) REVERT: A 163 ASN cc_start: 0.8145 (t0) cc_final: 0.7936 (t0) REVERT: C 321 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.8287 (m) REVERT: C 345 LEU cc_start: 0.3858 (OUTLIER) cc_final: 0.3639 (mt) outliers start: 30 outliers final: 19 residues processed: 220 average time/residue: 0.1434 time to fit residues: 48.1253 Evaluate side-chains 225 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 204 LYS Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 345 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 193 optimal weight: 2.9990 chunk 120 optimal weight: 0.0670 chunk 62 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 189 optimal weight: 0.4980 chunk 165 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.163634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.118803 restraints weight = 103656.797| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 6.18 r_work: 0.2634 rms_B_bonded: 5.97 restraints_weight: 2.0000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18139 Z= 0.126 Angle : 0.486 8.775 24867 Z= 0.259 Chirality : 0.045 0.171 2903 Planarity : 0.004 0.070 3006 Dihedral : 11.777 90.587 2982 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.88 % Allowed : 21.13 % Favored : 76.99 % 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: 0.34 (0.19), residues: 2094 helix: 0.56 (0.23), residues: 546 sheet: 0.55 (0.29), residues: 342 loop : 0.08 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 224 TYR 0.011 0.001 TYR A 225 PHE 0.024 0.001 PHE D 221 TRP 0.007 0.001 TRP B 86 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (18139) covalent geometry : angle 0.48604 / 0.26 (24867) hydrogen bonds : bond 0.03748 / 2.50 ( 637) hydrogen bonds : angle 5.32472 / 3.80 ( 1718) *********************** 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 239 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 210 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: D 264 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: B 104 MET cc_start: 0.9137 (mmm) cc_final: 0.8854 (tpt) REVERT: B 223 GLU cc_start: 0.8163 (tp30) cc_final: 0.7912 (tt0) REVERT: A 163 ASN cc_start: 0.8881 (t0) cc_final: 0.8543 (t0) REVERT: A 170 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7733 (mt-10) REVERT: A 345 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6551 (tp) REVERT: C 264 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7460 (mt-10) REVERT: C 321 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8295 (m) outliers start: 29 outliers final: 20 residues processed: 222 average time/residue: 0.1419 time to fit residues: 48.3610 Evaluate side-chains 226 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 85 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 111 optimal weight: 0.4980 chunk 162 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 191 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 117 optimal weight: 0.0060 chunk 12 optimal weight: 1.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 163 ASN E 136 ASN A 136 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.164827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.119825 restraints weight = 106564.583| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 6.27 r_work: 0.2618 rms_B_bonded: 6.09 restraints_weight: 2.0000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2552 r_free = 0.2552 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2552 r_free = 0.2552 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18139 Z= 0.133 Angle : 0.484 8.424 24867 Z= 0.258 Chirality : 0.045 0.142 2903 Planarity : 0.004 0.067 3006 Dihedral : 11.742 90.754 2982 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.15 % Allowed : 21.24 % Favored : 76.61 % 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: 0.34 (0.19), residues: 2094 helix: 0.58 (0.23), residues: 546 sheet: 0.60 (0.29), residues: 342 loop : 0.05 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 224 TYR 0.011 0.001 TYR A 225 PHE 0.031 0.001 PHE D 221 TRP 0.007 0.001 TRP B 86 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 (18139) covalent geometry : angle 0.48377 / 0.26 (24867) hydrogen bonds : bond 0.03653 / 2.42 ( 637) hydrogen bonds : angle 5.24323 / 3.74 ( 1718) *********************** REFINEMENT MACRO_CYCLE 6 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 242 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: D 109 LYS cc_start: 0.8734 (mmtm) cc_final: 0.8528 (mmtt) REVERT: D 264 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: D 330 MET cc_start: 0.7449 (mmt) cc_final: 0.7115 (mmp) REVERT: B 104 MET cc_start: 0.9129 (mmm) cc_final: 0.8847 (tpt) REVERT: B 223 GLU cc_start: 0.8134 (tp30) cc_final: 0.7842 (tt0) REVERT: A 163 ASN cc_start: 0.8894 (t0) cc_final: 0.8554 (t0) REVERT: A 170 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7698 (mt-10) REVERT: A 345 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6573 (tp) REVERT: C 264 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7424 (mt-10) REVERT: C 321 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8336 (m) REVERT: C 345 LEU cc_start: 0.3984 (OUTLIER) cc_final: 0.3685 (mt) outliers start: 34 outliers final: 23 residues processed: 224 average time/residue: 0.1182 time to fit residues: 40.6185 Evaluate side-chains 227 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 345 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 133 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 207 optimal weight: 30.0000 chunk 23 optimal weight: 0.8980 chunk 191 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 143 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 163 ASN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.164702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.119147 restraints weight = 106985.474| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 6.05 r_work: 0.2615 rms_B_bonded: 5.82 restraints_weight: 2.0000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 18139 Z= 0.176 Angle : 0.512 8.465 24867 Z= 0.271 Chirality : 0.046 0.144 2903 Planarity : 0.004 0.066 3006 Dihedral : 11.720 90.963 2982 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.15 % Allowed : 21.45 % Favored : 76.40 % 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: 0.26 (0.19), residues: 2094 helix: 0.50 (0.23), residues: 546 sheet: 0.58 (0.29), residues: 342 loop : -0.01 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 224 TYR 0.014 0.001 TYR A 225 PHE 0.026 0.002 PHE D 221 TRP 0.007 0.001 TRP B 86 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (18139) covalent geometry : angle 0.51165 / 0.27 (24867) hydrogen bonds : bond 0.03856 / 2.55 ( 637) hydrogen bonds : angle 5.32695 / 3.79 ( 1718) *********************** REFINEMENT MACRO_CYCLE 7 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 240 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: F 208 GLN cc_start: 0.8339 (tp-100) cc_final: 0.8017 (tp-100) REVERT: D 109 LYS cc_start: 0.8754 (mmtm) cc_final: 0.8550 (mmtt) REVERT: D 264 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7630 (tt0) REVERT: D 296 ASP cc_start: 0.8804 (t0) cc_final: 0.8363 (t0) REVERT: B 104 MET cc_start: 0.9136 (mmm) cc_final: 0.8858 (tpt) REVERT: B 147 SER cc_start: 0.8130 (p) cc_final: 0.7887 (p) REVERT: B 223 GLU cc_start: 0.8114 (tp30) cc_final: 0.7789 (tt0) REVERT: A 170 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7714 (mt-10) REVERT: A 345 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6550 (tp) REVERT: C 264 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7210 (mt-10) REVERT: C 321 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8373 (m) REVERT: C 345 LEU cc_start: 0.3938 (OUTLIER) cc_final: 0.3653 (mt) outliers start: 34 outliers final: 26 residues processed: 220 average time/residue: 0.1274 time to fit residues: 43.0715 Evaluate side-chains 229 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 204 LYS Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 345 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 162 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 170 optimal weight: 0.0770 chunk 204 optimal weight: 40.0000 chunk 6 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 163 ASN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.164640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.119837 restraints weight = 106081.920| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 6.25 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18139 Z= 0.127 Angle : 0.487 8.468 24867 Z= 0.258 Chirality : 0.045 0.146 2903 Planarity : 0.004 0.064 3006 Dihedral : 11.637 90.897 2982 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.10 % Allowed : 21.45 % Favored : 76.45 % 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: 0.29 (0.19), residues: 2094 helix: 0.56 (0.23), residues: 546 sheet: 0.56 (0.29), residues: 342 loop : 0.01 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 224 TYR 0.010 0.001 TYR A 225 PHE 0.031 0.001 PHE D 221 TRP 0.007 0.001 TRP B 86 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (18139) covalent geometry : angle 0.48698 / 0.26 (24867) hydrogen bonds : bond 0.03577 / 2.35 ( 637) hydrogen bonds : angle 5.18515 / 3.70 ( 1718) *********************** REFINEMENT MACRO_CYCLE 8 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: 33 poor density : 199 time to evaluate : 0.618 Fit side-chains REVERT: F 21 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7241 (mt-10) REVERT: F 208 GLN cc_start: 0.8490 (tp-100) cc_final: 0.8173 (tp-100) REVERT: D 109 LYS cc_start: 0.8466 (mmtm) cc_final: 0.8241 (mmtt) REVERT: E 204 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7528 (mtpp) REVERT: B 104 MET cc_start: 0.8672 (mmm) cc_final: 0.8396 (tpt) REVERT: B 147 SER cc_start: 0.8507 (p) cc_final: 0.8265 (p) REVERT: A 163 ASN cc_start: 0.8296 (t0) cc_final: 0.8082 (t0) REVERT: A 170 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7887 (mt-10) REVERT: A 259 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7404 (mttp) REVERT: A 345 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6370 (tp) REVERT: C 345 LEU cc_start: 0.3978 (OUTLIER) cc_final: 0.3759 (mt) outliers start: 33 outliers final: 21 residues processed: 215 average time/residue: 0.1239 time to fit residues: 40.4982 Evaluate side-chains 224 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 345 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 42 optimal weight: 0.0770 chunk 12 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 87 optimal weight: 0.0570 chunk 27 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 chunk 103 optimal weight: 0.4980 chunk 88 optimal weight: 0.6980 chunk 127 optimal weight: 0.4980 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.167809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.122542 restraints weight = 112955.815| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 5.99 r_work: 0.2689 rms_B_bonded: 5.27 restraints_weight: 2.0000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18139 Z= 0.096 Angle : 0.468 8.481 24867 Z= 0.250 Chirality : 0.044 0.205 2903 Planarity : 0.004 0.064 3006 Dihedral : 11.424 90.683 2979 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.77 % Allowed : 21.77 % Favored : 76.45 % 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: 0.38 (0.19), residues: 2094 helix: 0.68 (0.23), residues: 546 sheet: 0.58 (0.29), residues: 342 loop : 0.05 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 224 TYR 0.008 0.001 TYR E 225 PHE 0.031 0.001 PHE D 221 TRP 0.006 0.001 TRP B 86 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (18139) covalent geometry : angle 0.46757 / 0.25 (24867) hydrogen bonds : bond 0.03323 / 2.15 ( 637) hydrogen bonds : angle 4.99478 / 3.56 ( 1718) *********************** REFINEMENT MACRO_CYCLE 9 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 234 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: F 208 GLN cc_start: 0.8336 (tp-100) cc_final: 0.8029 (tp-100) REVERT: F 264 GLU cc_start: 0.7391 (mp0) cc_final: 0.6985 (mt-10) REVERT: D 109 LYS cc_start: 0.8677 (mmtm) cc_final: 0.8477 (mmtt) REVERT: D 296 ASP cc_start: 0.8671 (t0) cc_final: 0.8190 (t0) REVERT: D 304 GLU cc_start: 0.7030 (tm-30) cc_final: 0.6716 (tt0) REVERT: D 330 MET cc_start: 0.7306 (mmt) cc_final: 0.7034 (mmp) REVERT: E 254 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7229 (mp) REVERT: B 147 SER cc_start: 0.8089 (p) cc_final: 0.7850 (p) REVERT: A 163 ASN cc_start: 0.8794 (t0) cc_final: 0.8590 (t0) REVERT: A 170 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7645 (mt-10) REVERT: A 345 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6447 (tp) REVERT: C 264 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7385 (mt-10) REVERT: C 345 LEU cc_start: 0.4002 (OUTLIER) cc_final: 0.3725 (mt) outliers start: 27 outliers final: 20 residues processed: 222 average time/residue: 0.1221 time to fit residues: 41.6772 Evaluate side-chains 226 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 345 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 79 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 204 optimal weight: 40.0000 chunk 100 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 75 optimal weight: 0.3980 chunk 41 optimal weight: 0.0050 chunk 183 optimal weight: 0.0980 chunk 104 optimal weight: 0.0370 overall best weight: 0.2472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 163 ASN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN C 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.170515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.128445 restraints weight = 107163.494| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 7.56 r_work: 0.2705 rms_B_bonded: 5.31 restraints_weight: 2.0000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18139 Z= 0.090 Angle : 0.461 8.537 24867 Z= 0.246 Chirality : 0.044 0.167 2903 Planarity : 0.004 0.064 3006 Dihedral : 11.341 90.389 2979 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.88 % Allowed : 21.67 % Favored : 76.45 % 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: 0.44 (0.19), residues: 2094 helix: 0.73 (0.24), residues: 546 sheet: 0.62 (0.29), residues: 342 loop : 0.09 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 224 TYR 0.008 0.001 TYR E 225 PHE 0.031 0.001 PHE D 221 TRP 0.007 0.001 TRP A 86 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 (18139) covalent geometry : angle 0.46057 / 0.25 (24867) hydrogen bonds : bond 0.03191 / 2.06 ( 637) hydrogen bonds : angle 4.90499 / 3.49 ( 1718) ********************** REFINEMENT MACRO_CYCLE 10 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: 29 poor density : 209 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: F 208 GLN cc_start: 0.8237 (tp-100) cc_final: 0.7917 (tp-100) REVERT: D 109 LYS cc_start: 0.8641 (mmtm) cc_final: 0.8421 (mmtt) REVERT: D 152 GLN cc_start: 0.7591 (pm20) cc_final: 0.7124 (tp40) REVERT: D 330 MET cc_start: 0.7168 (mmt) cc_final: 0.6868 (mmp) REVERT: B 104 MET cc_start: 0.9099 (mmm) cc_final: 0.8812 (tpt) REVERT: B 147 SER cc_start: 0.7963 (p) cc_final: 0.7720 (p) REVERT: A 170 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7583 (mt-10) REVERT: A 345 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6362 (tp) REVERT: C 345 LEU cc_start: 0.3984 (OUTLIER) cc_final: 0.3696 (mt) outliers start: 29 outliers final: 23 residues processed: 222 average time/residue: 0.1187 time to fit residues: 40.5488 Evaluate side-chains 226 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 345 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 145 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 141 optimal weight: 0.1980 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 177 optimal weight: 0.0970 chunk 92 optimal weight: 0.4980 chunk 190 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 57 optimal weight: 0.0470 chunk 23 optimal weight: 0.5980 overall best weight: 0.2676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 163 ASN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.164183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.123629 restraints weight = 121139.244| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 4.60 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18139 Z= 0.088 Angle : 0.466 8.513 24867 Z= 0.249 Chirality : 0.044 0.198 2903 Planarity : 0.004 0.065 3006 Dihedral : 11.293 90.116 2979 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.83 % Allowed : 21.72 % Favored : 76.45 % 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: 0.48 (0.19), residues: 2094 helix: 0.75 (0.24), residues: 546 sheet: 0.67 (0.29), residues: 342 loop : 0.12 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 224 TYR 0.008 0.001 TYR E 225 PHE 0.033 0.001 PHE D 221 TRP 0.007 0.001 TRP B 86 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (18139) covalent geometry : angle 0.46569 / 0.25 (24867) hydrogen bonds : bond 0.03177 / 2.04 ( 637) hydrogen bonds : angle 4.87881 / 3.48 ( 1718) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3739.83 seconds wall clock time: 65 minutes 14.40 seconds (3914.40 seconds total)