Starting phenix.real_space_refine on Wed Jan 22 00:07:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ud5_42147/01_2025/8ud5_42147.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ud5_42147/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ud5_42147/01_2025/8ud5_42147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ud5_42147/01_2025/8ud5_42147.map" model { file = "/net/cci-nas-00/data/ceres_data/8ud5_42147/01_2025/8ud5_42147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ud5_42147/01_2025/8ud5_42147.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 16.38, per 1000 atoms: 0.93 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: 4.18 Conformation dependent library (CDL) restraints added in 3.8 seconds 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3924 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 46 sheets defined 26.3% alpha, 24.0% beta 20 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 6.82 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: 6.63 Time building geometry restraints manager: 4.87 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: 19.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 50.960 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.120 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.110 ------------------------------------------------------------------------------- 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= 0.138 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.001 TRP B 332 HIS 0.003 0.001 HIS B 337 PHE 0.027 0.001 PHE D 258 TYR 0.009 0.001 TYR A 342 ARG 0.004 0.000 ARG E 135 *********************** 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 : 1.774 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: 0.2967 time to fit residues: 99.7133 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 : 2.026 ------------------------------------------------------------------------------- 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 175 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 87 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 99 optimal weight: 0.0770 chunk 121 optimal weight: 0.6980 chunk 188 optimal weight: 0.1980 overall best weight: 0.3938 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.166752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.125914 restraints weight = 108227.522| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 4.50 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18139 Z= 0.158 Angle : 0.494 10.183 24867 Z= 0.264 Chirality : 0.044 0.175 2903 Planarity : 0.004 0.085 3006 Dihedral : 12.035 88.787 2985 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.61 % Allowed : 21.40 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.19), residues: 2094 helix: 0.76 (0.23), residues: 546 sheet: 0.73 (0.30), residues: 342 loop : 0.33 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 332 HIS 0.003 0.001 HIS B 337 PHE 0.010 0.001 PHE B 7 TYR 0.011 0.001 TYR A 225 ARG 0.006 0.000 ARG B 224 *********************** 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 260 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 231 time to evaluate : 1.922 Fit side-chains revert: symmetry clash REVERT: F 264 GLU cc_start: 0.7496 (mp0) cc_final: 0.7204 (mt-10) REVERT: D 152 GLN cc_start: 0.7611 (pm20) cc_final: 0.7346 (tp40) REVERT: D 183 ASP cc_start: 0.8041 (m-30) cc_final: 0.7738 (m-30) REVERT: B 104 MET cc_start: 0.8693 (mmm) cc_final: 0.8370 (tpt) REVERT: A 163 ASN cc_start: 0.8087 (t0) cc_final: 0.7776 (t0) REVERT: C 321 THR cc_start: 0.8365 (OUTLIER) cc_final: 0.8101 (m) outliers start: 29 outliers final: 15 residues processed: 241 average time/residue: 0.3014 time to fit residues: 109.9497 Evaluate side-chains 227 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 1.914 ------------------------------------------------------------------------------- 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 4 optimal weight: 0.1980 chunk 144 optimal weight: 0.0770 chunk 154 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 163 ASN B 175 GLN C 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.163170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.122274 restraints weight = 114956.284| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 4.38 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 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 = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1365 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= 0.230 Angle : 0.505 9.125 24867 Z= 0.265 Chirality : 0.045 0.159 2903 Planarity : 0.004 0.078 3006 Dihedral : 11.791 92.525 2982 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.83 % Allowed : 21.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.19), residues: 2094 helix: 0.67 (0.23), residues: 546 sheet: 0.73 (0.29), residues: 342 loop : 0.25 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 332 HIS 0.003 0.001 HIS B 337 PHE 0.012 0.001 PHE D 221 TYR 0.014 0.001 TYR A 225 ARG 0.006 0.000 ARG A 138 *********************** 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 241 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 211 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 104 MET cc_start: 0.8719 (mmm) cc_final: 0.8171 (tpt) REVERT: D 138 ARG cc_start: 0.8307 (mtp180) cc_final: 0.8002 (ttp-170) REVERT: B 16 ASP cc_start: 0.7735 (t70) cc_final: 0.7466 (t0) REVERT: B 104 MET cc_start: 0.8713 (mmm) cc_final: 0.8389 (tpt) REVERT: A 163 ASN cc_start: 0.8173 (t0) cc_final: 0.7860 (t0) REVERT: A 345 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6527 (tp) REVERT: C 321 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.8196 (m) outliers start: 30 outliers final: 17 residues processed: 220 average time/residue: 0.3214 time to fit residues: 107.6682 Evaluate side-chains 220 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 D residue 344 LYS 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 30 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 86 optimal weight: 0.4980 chunk 183 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 185 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 161 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** C 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.164315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.123377 restraints weight = 96695.843| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 4.39 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1560 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= 0.220 Angle : 0.496 8.743 24867 Z= 0.259 Chirality : 0.045 0.169 2903 Planarity : 0.004 0.072 3006 Dihedral : 11.679 92.514 2982 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.67 % Allowed : 21.45 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.19), residues: 2094 helix: 0.65 (0.23), residues: 546 sheet: 0.69 (0.29), residues: 342 loop : 0.17 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 332 HIS 0.004 0.001 HIS B 337 PHE 0.026 0.001 PHE D 221 TYR 0.012 0.001 TYR A 225 ARG 0.007 0.000 ARG A 138 *********************** 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 234 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 1.978 Fit side-chains revert: symmetry clash REVERT: F 208 GLN cc_start: 0.8631 (tp-100) cc_final: 0.8408 (tp-100) REVERT: D 138 ARG cc_start: 0.8285 (mtp180) cc_final: 0.8033 (ttp-170) REVERT: D 152 GLN cc_start: 0.7592 (pm20) cc_final: 0.7321 (tp40) REVERT: B 16 ASP cc_start: 0.7615 (t70) cc_final: 0.7339 (t0) REVERT: B 104 MET cc_start: 0.8712 (mmm) cc_final: 0.8394 (tpt) REVERT: A 345 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6537 (tp) outliers start: 26 outliers final: 16 residues processed: 219 average time/residue: 0.3253 time to fit residues: 109.6024 Evaluate side-chains 218 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 1.904 ------------------------------------------------------------------------------- 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 161 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 205 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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** B 18 GLN A 136 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.164071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.119677 restraints weight = 122110.117| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 5.52 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18139 Z= 0.254 Angle : 0.512 8.449 24867 Z= 0.266 Chirality : 0.045 0.171 2903 Planarity : 0.004 0.069 3006 Dihedral : 11.599 92.718 2982 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.94 % Allowed : 21.61 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.19), residues: 2094 helix: 0.58 (0.23), residues: 546 sheet: 0.67 (0.30), residues: 342 loop : 0.09 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 86 HIS 0.004 0.001 HIS B 337 PHE 0.030 0.002 PHE D 221 TYR 0.014 0.001 TYR A 225 ARG 0.006 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 1.920 Fit side-chains REVERT: F 208 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8288 (tp-100) REVERT: B 104 MET cc_start: 0.8687 (mmm) cc_final: 0.8387 (tpt) REVERT: A 345 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6433 (tp) REVERT: C 264 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6574 (mt-10) outliers start: 30 outliers final: 21 residues processed: 217 average time/residue: 0.2998 time to fit residues: 99.4676 Evaluate side-chains 218 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 320 VAL 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 85 optimal weight: 1.9990 chunk 169 optimal weight: 0.5980 chunk 176 optimal weight: 0.9980 chunk 107 optimal weight: 0.1980 chunk 68 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 0.0370 chunk 190 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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** A 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.167460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.122681 restraints weight = 104137.033| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 5.71 r_work: 0.2671 rms_B_bonded: 5.38 restraints_weight: 2.0000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18139 Z= 0.171 Angle : 0.481 8.359 24867 Z= 0.250 Chirality : 0.044 0.173 2903 Planarity : 0.004 0.065 3006 Dihedral : 11.359 91.857 2979 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.99 % Allowed : 21.67 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.19), residues: 2094 helix: 0.70 (0.23), residues: 546 sheet: 0.66 (0.29), residues: 342 loop : 0.12 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 86 HIS 0.004 0.001 HIS B 337 PHE 0.026 0.001 PHE D 221 TYR 0.009 0.001 TYR A 225 ARG 0.006 0.000 ARG B 224 *********************** 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 240 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 1.841 Fit side-chains revert: symmetry clash REVERT: F 208 GLN cc_start: 0.8382 (tp-100) cc_final: 0.8079 (tp-100) REVERT: D 296 ASP cc_start: 0.8734 (t0) cc_final: 0.8324 (t0) REVERT: E 204 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7604 (mtpp) REVERT: B 224 ARG cc_start: 0.7839 (ttm170) cc_final: 0.7529 (ttm-80) REVERT: A 163 ASN cc_start: 0.8784 (t0) cc_final: 0.8581 (t0) REVERT: A 170 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7687 (mt-10) outliers start: 31 outliers final: 25 residues processed: 223 average time/residue: 0.2933 time to fit residues: 100.8444 Evaluate side-chains 227 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 1.964 ------------------------------------------------------------------------------- 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 228 GLU 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 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain 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 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 155 VAL 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 132 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 142 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 108 optimal weight: 0.0470 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.166851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.121461 restraints weight = 112676.842| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 5.80 r_work: 0.2673 rms_B_bonded: 5.16 restraints_weight: 2.0000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1845 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= 0.197 Angle : 0.490 6.355 24867 Z= 0.254 Chirality : 0.044 0.173 2903 Planarity : 0.004 0.065 3006 Dihedral : 11.310 91.329 2979 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.20 % Allowed : 21.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.19), residues: 2094 helix: 0.68 (0.23), residues: 546 sheet: 0.67 (0.30), residues: 342 loop : 0.09 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 86 HIS 0.004 0.001 HIS B 337 PHE 0.032 0.001 PHE D 221 TYR 0.011 0.001 TYR A 225 ARG 0.005 0.000 ARG A 138 *********************** 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 238 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 1.891 Fit side-chains revert: symmetry clash REVERT: F 208 GLN cc_start: 0.8366 (tp-100) cc_final: 0.8072 (tp-100) REVERT: D 109 LYS cc_start: 0.8749 (mmtm) cc_final: 0.8542 (mmtt) REVERT: D 296 ASP cc_start: 0.8723 (t0) cc_final: 0.8289 (t0) REVERT: E 204 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7579 (mtpp) REVERT: E 254 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7262 (mp) REVERT: B 104 MET cc_start: 0.9129 (mmm) cc_final: 0.8865 (tpt) REVERT: A 170 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7697 (mt-10) REVERT: A 345 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6501 (tp) outliers start: 35 outliers final: 25 residues processed: 219 average time/residue: 0.2984 time to fit residues: 100.2326 Evaluate side-chains 228 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 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 204 LYS 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 202 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 155 VAL 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 130 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 177 optimal weight: 0.0370 chunk 166 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 201 optimal weight: 0.0060 chunk 186 optimal weight: 0.0170 chunk 176 optimal weight: 0.6980 overall best weight: 0.3112 ------------------------------------------------------------------------------- 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** A 136 ASN A 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.168215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.127330 restraints weight = 119791.748| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 4.56 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1979 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= 0.135 Angle : 0.462 6.507 24867 Z= 0.241 Chirality : 0.043 0.176 2903 Planarity : 0.003 0.064 3006 Dihedral : 11.174 89.263 2979 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.88 % Allowed : 21.67 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.19), residues: 2094 helix: 0.71 (0.23), residues: 552 sheet: 0.73 (0.29), residues: 342 loop : 0.18 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 86 HIS 0.004 0.001 HIS B 337 PHE 0.028 0.001 PHE D 221 TYR 0.008 0.001 TYR A 225 ARG 0.006 0.000 ARG B 224 *********************** 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 248 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 1.994 Fit side-chains REVERT: F 56 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.6944 (mp0) REVERT: F 208 GLN cc_start: 0.8517 (tp-100) cc_final: 0.8317 (tp-100) REVERT: F 264 GLU cc_start: 0.7407 (mp0) cc_final: 0.7165 (mt-10) REVERT: D 87 ASP cc_start: 0.8224 (t0) cc_final: 0.7927 (t0) REVERT: D 152 GLN cc_start: 0.7445 (pm20) cc_final: 0.7233 (tp40) REVERT: D 344 LYS cc_start: 0.6825 (ptmm) cc_final: 0.6154 (ptmm) REVERT: E 254 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7620 (mp) REVERT: E 296 ASP cc_start: 0.7970 (t0) cc_final: 0.7687 (t0) REVERT: B 224 ARG cc_start: 0.7968 (ttm170) cc_final: 0.7676 (ttm-80) REVERT: B 305 ILE cc_start: 0.8337 (mt) cc_final: 0.8103 (mt) REVERT: A 345 LEU cc_start: 0.6557 (OUTLIER) cc_final: 0.6220 (tp) outliers start: 29 outliers final: 24 residues processed: 232 average time/residue: 0.3037 time to fit residues: 107.5489 Evaluate side-chains 238 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 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 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 202 GLU Chi-restraints excluded: chain B residue 232 PHE 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 155 VAL Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 248 LEU 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 192 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 116 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 121 optimal weight: 0.0970 chunk 97 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 170 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.165364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.119726 restraints weight = 107723.472| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 6.15 r_work: 0.2624 rms_B_bonded: 6.01 restraints_weight: 2.0000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1986 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= 0.234 Angle : 0.500 6.562 24867 Z= 0.260 Chirality : 0.045 0.176 2903 Planarity : 0.004 0.065 3006 Dihedral : 11.235 87.971 2979 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.04 % Allowed : 21.88 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 2094 helix: 0.56 (0.23), residues: 552 sheet: 0.72 (0.30), residues: 342 loop : 0.11 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 332 HIS 0.004 0.001 HIS B 337 PHE 0.028 0.001 PHE D 221 TYR 0.013 0.001 TYR A 225 ARG 0.005 0.000 ARG B 224 *********************** 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 231 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 208 GLN cc_start: 0.8316 (tp-100) cc_final: 0.8021 (tp-100) REVERT: D 109 LYS cc_start: 0.8782 (mmtm) cc_final: 0.8580 (mmtt) REVERT: D 296 ASP cc_start: 0.8786 (t0) cc_final: 0.8383 (t0) REVERT: E 254 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7347 (mp) REVERT: B 104 MET cc_start: 0.9149 (mmm) cc_final: 0.8900 (tpt) REVERT: B 224 ARG cc_start: 0.7902 (ttm170) cc_final: 0.7590 (ttm-80) REVERT: A 170 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7667 (mt-10) REVERT: A 345 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6555 (tp) outliers start: 32 outliers final: 22 residues processed: 215 average time/residue: 0.2939 time to fit residues: 98.3988 Evaluate side-chains 219 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 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 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 155 VAL 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 40 optimal weight: 0.5980 chunk 178 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 7 optimal weight: 0.0970 chunk 107 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.166474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.123140 restraints weight = 109700.535| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 5.10 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18139 Z= 0.180 Angle : 0.490 6.715 24867 Z= 0.256 Chirality : 0.044 0.176 2903 Planarity : 0.004 0.064 3006 Dihedral : 11.227 86.887 2979 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.77 % Allowed : 22.10 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.19), residues: 2094 helix: 0.52 (0.23), residues: 552 sheet: 0.66 (0.30), residues: 342 loop : 0.11 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 86 HIS 0.004 0.001 HIS B 337 PHE 0.029 0.001 PHE D 221 TYR 0.010 0.001 TYR A 225 ARG 0.006 0.000 ARG B 224 ********************** 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 227 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 1.955 Fit side-chains revert: symmetry clash REVERT: F 208 GLN cc_start: 0.8523 (tp-100) cc_final: 0.8278 (tp-100) REVERT: D 109 LYS cc_start: 0.8508 (mmtm) cc_final: 0.8263 (mmtt) REVERT: D 344 LYS cc_start: 0.6851 (ptmm) cc_final: 0.6153 (ptmm) REVERT: E 254 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7586 (mp) REVERT: B 224 ARG cc_start: 0.8000 (ttm170) cc_final: 0.7667 (ttm-80) REVERT: A 170 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7777 (mt-10) REVERT: A 345 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.6392 (tp) outliers start: 27 outliers final: 22 residues processed: 214 average time/residue: 0.2973 time to fit residues: 98.6069 Evaluate side-chains 222 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 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 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 155 VAL 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 70 optimal weight: 0.3980 chunk 92 optimal weight: 0.0870 chunk 31 optimal weight: 0.0010 chunk 133 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 163 optimal weight: 0.9980 chunk 166 optimal weight: 0.9980 chunk 26 optimal weight: 0.0770 chunk 205 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 overall best weight: 0.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 187 GLN 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 = 0.3778 r_free = 0.3778 target = 0.169720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.128442 restraints weight = 110711.167| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 4.54 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18139 Z= 0.124 Angle : 0.468 8.650 24867 Z= 0.245 Chirality : 0.043 0.146 2903 Planarity : 0.003 0.062 3006 Dihedral : 11.160 86.385 2979 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.61 % Allowed : 22.20 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.19), residues: 2094 helix: 0.67 (0.23), residues: 552 sheet: 0.71 (0.29), residues: 342 loop : 0.18 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 86 HIS 0.004 0.001 HIS B 337 PHE 0.028 0.001 PHE D 221 TYR 0.007 0.001 TYR C 278 ARG 0.006 0.000 ARG B 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7428.65 seconds wall clock time: 134 minutes 1.25 seconds (8041.25 seconds total)