Starting phenix.real_space_refine on Sat Oct 11 20:36:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ud5_42147/10_2025/8ud5_42147.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ud5_42147/10_2025/8ud5_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_42147/10_2025/8ud5_42147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ud5_42147/10_2025/8ud5_42147.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ud5_42147/10_2025/8ud5_42147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ud5_42147/10_2025/8ud5_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/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: 7.53, per 1000 atoms: 0.43 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: 1.80 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 2.53 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: 3.52 Time building geometry restraints manager: 2.28 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=" O5' U G 7 " pdb=" C5' U G 7 " ideal model delta sigma weight residual 1.420 1.442 -0.022 1.50e-02 4.44e+03 2.16e+00 bond pdb=" CB PRO A 262 " pdb=" CG PRO A 262 " ideal model delta sigma weight residual 1.492 1.564 -0.072 5.00e-02 4.00e+02 2.09e+00 bond pdb=" O5' U G 5 " pdb=" C5' U G 5 " ideal model delta sigma weight residual 1.420 1.442 -0.022 1.50e-02 4.44e+03 2.08e+00 bond pdb=" O5' A H 29 " pdb=" C5' A H 29 " ideal model delta sigma weight residual 1.420 1.441 -0.021 1.50e-02 4.44e+03 2.01e+00 ... (remaining 18134 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 24598 1.91 - 3.81: 242 3.81 - 5.72: 22 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=" C4' U G 4 " pdb=" C3' U G 4 " pdb=" O3' U G 4 " ideal model delta sigma weight residual 113.00 107.58 5.42 1.50e+00 4.44e-01 1.30e+01 angle pdb=" C4' A H 26 " pdb=" C3' A H 26 " pdb=" O3' A H 26 " ideal model delta sigma weight residual 113.00 107.91 5.09 1.50e+00 4.44e-01 1.15e+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 ... (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: 2255 0.047 - 0.095: 427 0.095 - 0.142: 193 0.142 - 0.190: 23 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: 6.940 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.300 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 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= 0.116 Angle : 0.490 9.534 24867 Z= 0.283 Chirality : 0.046 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 aren 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 covalent geometry : bond 0.00220 (18139) covalent geometry : angle 0.48957 (24867) hydrogen bonds : bond 0.20642 ( 637) hydrogen bonds : angle 8.36966 ( 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 : 0.663 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: 0.1444 time to fit residues: 48.7245 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 : 0.704 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN B 187 GLN A 199 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.165077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.124188 restraints weight = 112221.105| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 4.42 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18139 Z= 0.120 Angle : 0.498 10.299 24867 Z= 0.267 Chirality : 0.044 0.170 2903 Planarity : 0.004 0.087 3006 Dihedral : 12.055 89.062 2985 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.61 % Allowed : 21.29 % 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 aren not related in a simple way. whole: 0.65 (0.19), residues: 2094 helix: 0.74 (0.23), residues: 546 sheet: 0.74 (0.30), residues: 342 loop : 0.32 (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 0.010 0.001 PHE D 7 TRP 0.008 0.001 TRP D 332 HIS 0.003 0.001 HIS B 337 Details of bonding type rmsd covalent geometry : bond 0.00273 (18139) covalent geometry : angle 0.49797 (24867) hydrogen bonds : bond 0.04017 ( 637) hydrogen bonds : angle 5.74484 ( 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 250 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 221 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: F 264 GLU cc_start: 0.7486 (mp0) cc_final: 0.7194 (mt-10) REVERT: D 152 GLN cc_start: 0.7622 (pm20) cc_final: 0.7350 (tp40) REVERT: B 104 MET cc_start: 0.8670 (mmm) cc_final: 0.8343 (tpt) REVERT: B 277 ASN cc_start: 0.8530 (m-40) cc_final: 0.8300 (m-40) REVERT: A 163 ASN cc_start: 0.8134 (t0) cc_final: 0.7827 (t0) REVERT: C 321 THR cc_start: 0.8360 (OUTLIER) cc_final: 0.8094 (m) outliers start: 29 outliers final: 15 residues processed: 231 average time/residue: 0.1495 time to fit residues: 52.6844 Evaluate side-chains 222 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 155 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 321 THR 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 B residue 96 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain C residue 96 ILE 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: 1.9990 chunk 67 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 205 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 104 optimal weight: 0.0970 chunk 83 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 163 ASN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN A 74 ASN C 187 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.162180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.121008 restraints weight = 110164.163| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 4.29 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18139 Z= 0.167 Angle : 0.521 9.208 24867 Z= 0.273 Chirality : 0.046 0.160 2903 Planarity : 0.004 0.079 3006 Dihedral : 11.826 92.632 2982 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.77 % Allowed : 21.56 % Favored : 76.67 % 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 aren not related in a simple way. whole: 0.49 (0.19), residues: 2094 helix: 0.59 (0.23), residues: 546 sheet: 0.72 (0.30), residues: 342 loop : 0.20 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 224 TYR 0.016 0.001 TYR A 225 PHE 0.012 0.002 PHE F 134 TRP 0.007 0.001 TRP D 332 HIS 0.003 0.001 HIS B 337 Details of bonding type rmsd covalent geometry : bond 0.00406 (18139) covalent geometry : angle 0.52084 (24867) hydrogen bonds : bond 0.04003 ( 637) hydrogen bonds : angle 5.54307 ( 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 237 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: D 104 MET cc_start: 0.8762 (mmm) cc_final: 0.8225 (tpt) REVERT: B 104 MET cc_start: 0.8714 (mmm) cc_final: 0.8390 (tpt) REVERT: B 277 ASN cc_start: 0.8779 (m-40) cc_final: 0.8499 (m-40) REVERT: A 163 ASN cc_start: 0.8184 (t0) cc_final: 0.7874 (t0) REVERT: A 345 LEU cc_start: 0.6847 (OUTLIER) cc_final: 0.6512 (tp) REVERT: C 321 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8212 (m) outliers start: 29 outliers final: 15 residues processed: 219 average time/residue: 0.1498 time to fit residues: 50.2050 Evaluate side-chains 212 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 285 THR 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 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 A residue 209 MET Chi-restraints excluded: chain A residue 345 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 63 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 35 optimal weight: 0.0770 chunk 18 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 163 ASN B 18 GLN C 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.163626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.122818 restraints weight = 109767.765| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 4.36 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 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 = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1544 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= 0.133 Angle : 0.492 8.905 24867 Z= 0.257 Chirality : 0.044 0.169 2903 Planarity : 0.004 0.073 3006 Dihedral : 11.635 92.585 2982 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.88 % Allowed : 21.40 % Favored : 76.72 % 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 aren not related in a simple way. whole: 0.47 (0.19), residues: 2094 helix: 0.62 (0.23), residues: 546 sheet: 0.70 (0.29), residues: 342 loop : 0.16 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 138 TYR 0.011 0.001 TYR A 225 PHE 0.026 0.001 PHE D 221 TRP 0.007 0.001 TRP D 332 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd covalent geometry : bond 0.00319 (18139) covalent geometry : angle 0.49198 (24867) hydrogen bonds : bond 0.03514 ( 637) hydrogen bonds : angle 5.24168 ( 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 235 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: F 208 GLN cc_start: 0.8643 (tp-100) cc_final: 0.8432 (tp-100) REVERT: D 109 LYS cc_start: 0.8544 (mmtm) cc_final: 0.8330 (mmtt) REVERT: D 152 GLN cc_start: 0.7595 (pm20) cc_final: 0.7334 (tp40) REVERT: B 16 ASP cc_start: 0.7581 (t0) cc_final: 0.7323 (t0) REVERT: B 104 MET cc_start: 0.8707 (mmm) cc_final: 0.8396 (tpt) REVERT: B 277 ASN cc_start: 0.8658 (m-40) cc_final: 0.8418 (m-40) REVERT: A 345 LEU cc_start: 0.6622 (OUTLIER) cc_final: 0.6309 (tp) outliers start: 30 outliers final: 16 residues processed: 219 average time/residue: 0.1471 time to fit residues: 49.3730 Evaluate side-chains 221 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 232 PHE 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 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 232 PHE Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 250 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 193 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 58 optimal weight: 0.0970 chunk 189 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 163 ASN E 136 ASN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.166762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.121349 restraints weight = 103105.893| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 6.10 r_work: 0.2641 rms_B_bonded: 5.82 restraints_weight: 2.0000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2584 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2584 r_free = 0.2584 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2584 r_free = 0.2584 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1647 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= 0.129 Angle : 0.493 8.528 24867 Z= 0.256 Chirality : 0.044 0.172 2903 Planarity : 0.004 0.069 3006 Dihedral : 11.570 92.495 2982 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.61 % Allowed : 21.72 % Favored : 76.67 % 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 aren not related in a simple way. whole: 0.46 (0.19), residues: 2094 helix: 0.63 (0.23), residues: 546 sheet: 0.68 (0.29), residues: 342 loop : 0.15 (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 0.029 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 covalent geometry : bond 0.00308 (18139) covalent geometry : angle 0.49302 (24867) hydrogen bonds : bond 0.03426 ( 637) hydrogen bonds : angle 5.14315 ( 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 225 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 0.724 Fit side-chains REVERT: F 208 GLN cc_start: 0.8369 (tp-100) cc_final: 0.8102 (tp-100) REVERT: E 254 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7368 (mp) REVERT: B 104 MET cc_start: 0.9139 (mmm) cc_final: 0.8865 (tpt) REVERT: B 277 ASN cc_start: 0.9080 (m-40) cc_final: 0.8658 (m-40) REVERT: A 345 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6575 (tp) REVERT: C 345 LEU cc_start: 0.3979 (OUTLIER) cc_final: 0.3715 (mt) outliers start: 24 outliers final: 17 residues processed: 212 average time/residue: 0.1458 time to fit residues: 47.3786 Evaluate side-chains 217 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 321 THR 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 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 232 PHE 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 345 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 85 optimal weight: 2.9990 chunk 4 optimal weight: 0.0040 chunk 110 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 178 optimal weight: 0.7980 chunk 191 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 163 ASN 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 = 0.3714 r_free = 0.3714 target = 0.163559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.122484 restraints weight = 107974.919| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 4.40 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1751 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= 0.137 Angle : 0.493 8.595 24867 Z= 0.256 Chirality : 0.045 0.173 2903 Planarity : 0.004 0.066 3006 Dihedral : 11.383 91.817 2979 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.26 % Allowed : 21.13 % 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 aren not related in a simple way. whole: 0.45 (0.19), residues: 2094 helix: 0.63 (0.23), residues: 546 sheet: 0.71 (0.30), residues: 342 loop : 0.12 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 138 TYR 0.012 0.001 TYR A 225 PHE 0.027 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 covalent geometry : bond 0.00329 (18139) covalent geometry : angle 0.49323 (24867) hydrogen bonds : bond 0.03433 ( 637) hydrogen bonds : angle 5.11505 ( 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 235 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: F 208 GLN cc_start: 0.8669 (tp-100) cc_final: 0.8445 (tp-100) REVERT: D 296 ASP cc_start: 0.8257 (t0) cc_final: 0.7993 (t0) REVERT: E 254 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7628 (mp) REVERT: B 104 MET cc_start: 0.8712 (mmm) cc_final: 0.8398 (tpt) REVERT: B 224 ARG cc_start: 0.8033 (ttm170) cc_final: 0.7730 (ttm-80) REVERT: A 163 ASN cc_start: 0.8132 (t0) cc_final: 0.7881 (t0) REVERT: A 345 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6461 (tp) outliers start: 36 outliers final: 24 residues processed: 221 average time/residue: 0.1479 time to fit residues: 49.8455 Evaluate side-chains 219 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 232 PHE Chi-restraints excluded: chain F residue 320 VAL 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 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 232 PHE Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain A residue 51 VAL 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 133 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 207 optimal weight: 10.9990 chunk 23 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 20 optimal weight: 0.0170 overall best weight: 1.1224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3703 r_free = 0.3703 target = 0.162081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.116379 restraints weight = 107311.681| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 6.24 r_work: 0.2591 rms_B_bonded: 5.97 restraints_weight: 2.0000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 18139 Z= 0.196 Angle : 0.533 6.450 24867 Z= 0.277 Chirality : 0.046 0.171 2903 Planarity : 0.004 0.067 3006 Dihedral : 11.408 91.265 2979 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.99 % Allowed : 21.18 % Favored : 76.83 % 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 aren not related in a simple way. whole: 0.27 (0.19), residues: 2094 helix: 0.46 (0.23), residues: 546 sheet: 0.66 (0.30), 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 0.014 0.001 TYR A 225 PHE 0.029 0.002 PHE D 221 TRP 0.006 0.001 TRP B 332 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd covalent geometry : bond 0.00481 (18139) covalent geometry : angle 0.53260 (24867) hydrogen bonds : bond 0.03819 ( 637) hydrogen bonds : angle 5.33040 ( 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 230 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 208 GLN cc_start: 0.8336 (tp-100) cc_final: 0.8009 (tp-100) REVERT: D 296 ASP cc_start: 0.8843 (t0) cc_final: 0.8420 (t0) REVERT: E 254 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7305 (mp) REVERT: B 104 MET cc_start: 0.9158 (mmm) cc_final: 0.8889 (tpt) REVERT: B 147 SER cc_start: 0.8145 (p) cc_final: 0.7884 (p) REVERT: A 163 ASN cc_start: 0.8886 (t0) cc_final: 0.8675 (t0) REVERT: A 170 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: A 233 GLU cc_start: 0.8432 (mp0) cc_final: 0.8217 (mp0) REVERT: A 345 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6573 (tp) outliers start: 31 outliers final: 22 residues processed: 214 average time/residue: 0.1422 time to fit residues: 46.7018 Evaluate side-chains 221 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 320 VAL 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 254 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 252 ILE 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 162 optimal weight: 0.0040 chunk 135 optimal weight: 10.0000 chunk 170 optimal weight: 0.0980 chunk 204 optimal weight: 10.9990 chunk 6 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 123 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN A 74 ASN A 136 ASN A 187 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.167299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.122341 restraints weight = 106375.443| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 6.12 r_work: 0.2671 rms_B_bonded: 5.87 restraints_weight: 2.0000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1940 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= 0.099 Angle : 0.466 6.531 24867 Z= 0.244 Chirality : 0.043 0.174 2903 Planarity : 0.004 0.065 3006 Dihedral : 11.229 89.224 2979 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.72 % Allowed : 21.61 % Favored : 76.67 % 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 aren not related in a simple way. whole: 0.46 (0.19), residues: 2094 helix: 0.68 (0.23), residues: 546 sheet: 0.72 (0.30), residues: 342 loop : 0.11 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 224 TYR 0.008 0.001 TYR F 237 PHE 0.028 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 covalent geometry : bond 0.00227 (18139) covalent geometry : angle 0.46625 (24867) hydrogen bonds : bond 0.03120 ( 637) hydrogen bonds : angle 4.87700 ( 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 246 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 220 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 208 GLN cc_start: 0.8344 (tp-100) cc_final: 0.8034 (tp-100) REVERT: F 264 GLU cc_start: 0.7475 (mp0) cc_final: 0.7092 (mt-10) REVERT: D 296 ASP cc_start: 0.8754 (t0) cc_final: 0.8345 (t0) REVERT: D 344 LYS cc_start: 0.6794 (ptmm) cc_final: 0.6031 (ptmm) REVERT: E 254 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7299 (mp) REVERT: B 147 SER cc_start: 0.7992 (p) cc_final: 0.7756 (p) REVERT: B 224 ARG cc_start: 0.7877 (ttm170) cc_final: 0.7561 (ttm-80) REVERT: B 305 ILE cc_start: 0.8242 (mt) cc_final: 0.8033 (mt) REVERT: A 163 ASN cc_start: 0.8824 (t0) cc_final: 0.8615 (t0) REVERT: A 170 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7730 (mt-10) REVERT: A 296 ASP cc_start: 0.8526 (t0) cc_final: 0.8223 (t0) REVERT: C 163 ASN cc_start: 0.8731 (m-40) cc_final: 0.8513 (m-40) outliers start: 26 outliers final: 20 residues processed: 232 average time/residue: 0.1464 time to fit residues: 51.7912 Evaluate side-chains 228 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 232 PHE Chi-restraints excluded: chain F residue 320 VAL 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 232 PHE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 114 THR 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 42 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 chunk 27 optimal weight: 0.0170 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 127 optimal weight: 0.0870 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3769 r_free = 0.3769 target = 0.168369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.123528 restraints weight = 113469.262| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 5.99 r_work: 0.2675 rms_B_bonded: 5.74 restraints_weight: 2.0000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1995 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= 0.104 Angle : 0.474 6.574 24867 Z= 0.247 Chirality : 0.044 0.175 2903 Planarity : 0.004 0.064 3006 Dihedral : 11.210 88.026 2979 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.67 % Allowed : 21.51 % Favored : 76.83 % 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 aren not related in a simple way. whole: 0.52 (0.19), residues: 2094 helix: 0.73 (0.23), residues: 546 sheet: 0.76 (0.30), residues: 342 loop : 0.14 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 224 TYR 0.009 0.001 TYR A 225 PHE 0.028 0.001 PHE D 221 TRP 0.006 0.001 TRP A 86 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd covalent geometry : bond 0.00241 (18139) covalent geometry : angle 0.47443 (24867) hydrogen bonds : bond 0.03197 ( 637) hydrogen bonds : angle 4.87161 ( 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 232 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 208 GLN cc_start: 0.8354 (tp-100) cc_final: 0.8040 (tp-100) REVERT: F 264 GLU cc_start: 0.7396 (mp0) cc_final: 0.7020 (mt-10) REVERT: D 109 LYS cc_start: 0.8567 (mmtt) cc_final: 0.8315 (mmtt) REVERT: D 344 LYS cc_start: 0.6751 (ptmm) cc_final: 0.5984 (ptmm) REVERT: E 254 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7255 (mp) REVERT: B 147 SER cc_start: 0.8013 (p) cc_final: 0.7777 (p) REVERT: B 224 ARG cc_start: 0.7894 (ttm170) cc_final: 0.7567 (ttm-80) REVERT: B 284 GLN cc_start: 0.8329 (tt0) cc_final: 0.8077 (tt0) REVERT: B 339 GLU cc_start: 0.7461 (tt0) cc_final: 0.7001 (mt-10) REVERT: A 163 ASN cc_start: 0.8828 (t0) cc_final: 0.8627 (t0) REVERT: A 170 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7721 (mt-10) REVERT: A 233 GLU cc_start: 0.8363 (mp0) cc_final: 0.7941 (mm-30) REVERT: A 296 ASP cc_start: 0.8536 (t0) cc_final: 0.8291 (t0) REVERT: C 158 LYS cc_start: 0.8949 (mttm) cc_final: 0.8714 (mttt) outliers start: 25 outliers final: 19 residues processed: 221 average time/residue: 0.1507 time to fit residues: 50.6418 Evaluate side-chains 227 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 232 PHE 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 254 LEU 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 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 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: 1.9990 chunk 123 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 204 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 183 optimal weight: 0.8980 chunk 104 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 163 ASN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN C 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.165794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.123085 restraints weight = 108061.217| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 4.95 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2020 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= 0.134 Angle : 0.496 8.622 24867 Z= 0.258 Chirality : 0.044 0.212 2903 Planarity : 0.004 0.064 3006 Dihedral : 11.248 86.667 2979 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.56 % Allowed : 21.77 % Favored : 76.67 % 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 aren not related in a simple way. whole: 0.43 (0.19), residues: 2094 helix: 0.63 (0.23), residues: 546 sheet: 0.75 (0.30), residues: 342 loop : 0.09 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 224 TYR 0.012 0.001 TYR A 225 PHE 0.028 0.001 PHE D 221 TRP 0.006 0.001 TRP F 332 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd covalent geometry : bond 0.00324 (18139) covalent geometry : angle 0.49613 (24867) hydrogen bonds : bond 0.03433 ( 637) hydrogen bonds : angle 5.00843 ( 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 224 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 208 GLN cc_start: 0.8600 (tp-100) cc_final: 0.8338 (tp-100) REVERT: D 296 ASP cc_start: 0.8218 (t0) cc_final: 0.7939 (t0) REVERT: D 344 LYS cc_start: 0.6833 (ptmm) cc_final: 0.6183 (ptmm) REVERT: B 104 MET cc_start: 0.8711 (mmm) cc_final: 0.8438 (tpt) REVERT: B 147 SER cc_start: 0.8541 (p) cc_final: 0.8315 (p) REVERT: B 224 ARG cc_start: 0.8010 (ttm170) cc_final: 0.7675 (ttm-80) REVERT: B 284 GLN cc_start: 0.8178 (tt0) cc_final: 0.7937 (tt0) REVERT: A 163 ASN cc_start: 0.8141 (t0) cc_final: 0.7931 (t0) REVERT: A 170 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7826 (mt-10) REVERT: A 345 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6434 (tp) REVERT: C 158 LYS cc_start: 0.8429 (mttm) cc_final: 0.8195 (mttt) outliers start: 23 outliers final: 19 residues processed: 213 average time/residue: 0.1480 time to fit residues: 48.1280 Evaluate side-chains 218 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 232 PHE 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 254 LEU 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 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: 0.7980 chunk 141 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 177 optimal weight: 0.0000 chunk 92 optimal weight: 2.9990 chunk 190 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 163 ASN E 136 ASN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN C 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.166383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.123082 restraints weight = 119615.942| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 5.14 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18139 Z= 0.119 Angle : 0.487 7.851 24867 Z= 0.254 Chirality : 0.044 0.198 2903 Planarity : 0.004 0.064 3006 Dihedral : 11.247 85.437 2979 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.94 % Allowed : 21.67 % 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 aren not related in a simple way. whole: 0.43 (0.19), residues: 2094 helix: 0.62 (0.23), residues: 546 sheet: 0.73 (0.30), residues: 342 loop : 0.10 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 224 TYR 0.009 0.001 TYR A 225 PHE 0.031 0.001 PHE D 221 TRP 0.006 0.001 TRP F 332 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd covalent geometry : bond 0.00284 (18139) covalent geometry : angle 0.48711 (24867) hydrogen bonds : bond 0.03316 ( 637) hydrogen bonds : angle 4.95695 ( 1718) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4053.98 seconds wall clock time: 70 minutes 42.29 seconds (4242.29 seconds total)