Starting phenix.real_space_refine on Sun Aug 24 05:10:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ud3_42145/08_2025/8ud3_42145.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ud3_42145/08_2025/8ud3_42145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ud3_42145/08_2025/8ud3_42145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ud3_42145/08_2025/8ud3_42145.map" model { file = "/net/cci-nas-00/data/ceres_data/8ud3_42145/08_2025/8ud3_42145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ud3_42145/08_2025/8ud3_42145.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 34 5.49 5 S 60 5.16 5 C 10943 2.51 5 N 2807 2.21 5 O 3400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17244 Number of models: 1 Model: "" Number of chains: 8 Chain: "F" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "D" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "E" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "B" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "A" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "C" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "G" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 340 Classifications: {'RNA': 17} Modifications used: {'rna3p_pyr': 17} Link IDs: {'rna3p': 16} Chain: "H" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 374 Classifications: {'RNA': 17} Modifications used: {'rna3p_pur': 17} Link IDs: {'rna3p': 16} Residues with excluded nonbonded symmetry interactions: 18 residue: pdb=" N AILE F 27 " occ=0.52 ... (14 atoms not shown) pdb=" CD1BILE F 27 " occ=0.48 residue: pdb=" N AASN F 28 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN F 28 " occ=0.48 residue: pdb=" N AASN F 29 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN F 29 " occ=0.48 residue: pdb=" N AILE D 27 " occ=0.52 ... (14 atoms not shown) pdb=" CD1BILE D 27 " occ=0.48 residue: pdb=" N AASN D 28 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN D 28 " occ=0.48 residue: pdb=" N AASN D 29 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN D 29 " occ=0.48 residue: pdb=" N AILE E 27 " occ=0.52 ... (14 atoms not shown) pdb=" CD1BILE E 27 " occ=0.48 residue: pdb=" N AASN E 28 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN E 28 " occ=0.48 residue: pdb=" N AASN E 29 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN E 29 " occ=0.48 residue: pdb=" N AILE B 27 " occ=0.52 ... (14 atoms not shown) pdb=" CD1BILE B 27 " occ=0.48 residue: pdb=" N AASN B 28 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN B 28 " occ=0.48 residue: pdb=" N AASN B 29 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN B 29 " occ=0.48 ... (remaining 6 not shown) Time building chain proxies: 6.77, per 1000 atoms: 0.39 Number of scatterers: 17244 At special positions: 0 Unit cell: (114.08, 122.36, 133.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 34 15.00 O 3400 8.00 N 2807 7.00 C 10943 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3924 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 47 sheets defined 26.8% alpha, 24.6% beta 15 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'F' and resid 1 through 13 Processing helix chain 'F' and resid 50 through 60 Processing helix chain 'F' and resid 68 through 75 Processing helix chain 'F' and resid 113 through 117 Processing helix chain 'F' and resid 129 through 137 Processing helix chain 'F' and resid 207 through 216 Processing helix chain 'F' and resid 217 through 225 Processing helix chain 'F' and resid 231 through 236 Processing helix chain 'F' and resid 250 through 261 removed outlier: 3.567A pdb=" N GLU F 260 " --> pdb=" O LYS F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 308 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 50 through 60 Processing helix chain 'D' and resid 68 through 75 Processing helix chain 'D' and resid 113 through 117 Processing helix chain 'D' and resid 129 through 137 Processing helix chain 'D' and resid 207 through 216 Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 231 through 236 removed outlier: 3.509A pdb=" N VAL D 236 " --> pdb=" O PHE D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.589A pdb=" N GLU D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 50 through 60 Processing helix chain 'E' and resid 68 through 75 Processing helix chain 'E' and resid 113 through 117 Processing helix chain 'E' and resid 129 through 136 Processing helix chain 'E' and resid 207 through 216 Processing helix chain 'E' and resid 217 through 225 Processing helix chain 'E' and resid 231 through 236 Processing helix chain 'E' and resid 250 through 261 removed outlier: 3.526A pdb=" N GLU E 260 " --> pdb=" O LYS E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 308 Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 50 through 60 Processing helix chain 'B' and resid 68 through 75 Processing helix chain 'B' and resid 113 through 117 Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 207 through 216 Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.550A pdb=" N GLU B 260 " --> pdb=" O LYS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 68 through 75 Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.665A pdb=" N GLU A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 308 Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 50 through 60 Processing helix chain 'C' and resid 68 through 75 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 129 through 136 Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.637A pdb=" N GLU C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 308 Processing sheet with id=AA1, first strand: chain 'F' and resid 24 through 27 removed outlier: 6.567A pdb=" N VAL F 31 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 79 through 80 removed outlier: 7.086A pdb=" N ILE F 79 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N ASP F 124 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LYS F 180 " --> pdb=" O GLN F 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'F' and resid 98 through 99 removed outlier: 8.036A pdb=" N THR F 98 " --> pdb=" O ILE F 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AA6, first strand: chain 'F' and resid 264 through 266 removed outlier: 4.958A pdb=" N ILE F 280 " --> pdb=" O CYS F 290 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N CYS F 290 " --> pdb=" O ILE F 280 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 315 through 322 removed outlier: 7.345A pdb=" N SER F 328 " --> pdb=" O PRO F 343 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N MET F 330 " --> pdb=" O PHE F 341 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE F 341 " --> pdb=" O MET F 330 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP F 332 " --> pdb=" O GLU F 339 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 24 through 27 removed outlier: 6.605A pdb=" N VAL D 31 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 79 through 80 removed outlier: 7.194A pdb=" N ILE D 79 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ASP D 124 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 79 through 80 removed outlier: 7.194A pdb=" N ILE D 79 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ASP D 124 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS D 180 " --> pdb=" O GLN D 187 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 86 through 87 Processing sheet with id=AB3, first strand: chain 'D' and resid 98 through 99 removed outlier: 8.016A pdb=" N THR D 98 " --> pdb=" O ILE D 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 160 through 162 Processing sheet with id=AB5, first strand: chain 'D' and resid 264 through 266 removed outlier: 4.949A pdb=" N ILE D 280 " --> pdb=" O CYS D 290 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N CYS D 290 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 315 through 322 removed outlier: 5.863A pdb=" N LYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL D 338 " --> pdb=" O LYS D 334 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 24 through 27 removed outlier: 6.594A pdb=" N VAL E 31 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.098A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N ASP E 124 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.098A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N ASP E 124 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LYS E 180 " --> pdb=" O GLN E 187 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AC2, first strand: chain 'E' and resid 98 through 99 removed outlier: 8.124A pdb=" N THR E 98 " --> pdb=" O ILE E 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 160 through 162 Processing sheet with id=AC4, first strand: chain 'E' and resid 264 through 266 removed outlier: 4.973A pdb=" N ILE E 280 " --> pdb=" O CYS E 290 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N CYS E 290 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 315 through 322 removed outlier: 7.154A pdb=" N SER E 328 " --> pdb=" O PRO E 343 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N MET E 330 " --> pdb=" O PHE E 341 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE E 341 " --> pdb=" O MET E 330 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP E 332 " --> pdb=" O GLU E 339 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 24 through 27 removed outlier: 6.634A pdb=" N VAL B 31 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.133A pdb=" N ILE B 79 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ASP B 124 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.133A pdb=" N ILE B 79 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ASP B 124 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LYS B 180 " --> pdb=" O GLN B 187 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AD1, first strand: chain 'B' and resid 98 through 99 removed outlier: 8.114A pdb=" N THR B 98 " --> pdb=" O ILE B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AD3, first strand: chain 'B' and resid 264 through 266 removed outlier: 4.935A pdb=" N ILE B 280 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N CYS B 290 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 315 through 322 removed outlier: 7.198A pdb=" N SER B 328 " --> pdb=" O PRO B 343 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N MET B 330 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE B 341 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP B 332 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 24 through 26 removed outlier: 6.651A pdb=" N VAL A 31 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.082A pdb=" N ILE A 79 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ASP A 124 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.082A pdb=" N ILE A 79 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ASP A 124 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS A 180 " --> pdb=" O GLN A 187 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AD9, first strand: chain 'A' and resid 98 through 99 removed outlier: 8.093A pdb=" N THR A 98 " --> pdb=" O ILE A 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AE2, first strand: chain 'A' and resid 264 through 266 removed outlier: 5.000A pdb=" N ILE A 280 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N CYS A 290 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 316 through 322 removed outlier: 3.956A pdb=" N TYR A 342 " --> pdb=" O MET A 330 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 24 through 26 removed outlier: 6.599A pdb=" N VAL C 31 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.129A pdb=" N ILE C 79 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N ASP C 124 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.129A pdb=" N ILE C 79 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N ASP C 124 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LYS C 180 " --> pdb=" O GLN C 187 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AE8, first strand: chain 'C' and resid 98 through 99 removed outlier: 8.042A pdb=" N THR C 98 " --> pdb=" O ILE C 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 160 through 162 Processing sheet with id=AF1, first strand: chain 'C' and resid 264 through 266 removed outlier: 4.792A pdb=" N ILE C 280 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N CYS C 290 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 315 through 322 removed outlier: 7.117A pdb=" N SER C 328 " --> pdb=" O PRO C 343 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N MET C 330 " --> pdb=" O PHE C 341 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE C 341 " --> pdb=" O MET C 330 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP C 332 " --> pdb=" O GLU C 339 " (cutoff:3.500A) 650 hydrogen bonds defined for protein. 1668 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 3.36 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4847 1.33 - 1.45: 2870 1.45 - 1.57: 9796 1.57 - 1.69: 66 1.69 - 1.81: 90 Bond restraints: 17669 Sorted by residual: bond pdb=" CA SER C 261 " pdb=" CB SER C 261 " ideal model delta sigma weight residual 1.526 1.503 0.024 9.30e-03 1.16e+04 6.41e+00 bond pdb=" CA PHE C 263 " pdb=" C PHE C 263 " ideal model delta sigma weight residual 1.524 1.492 0.033 1.35e-02 5.49e+03 5.82e+00 bond pdb=" C SER C 261 " pdb=" O SER C 261 " ideal model delta sigma weight residual 1.241 1.220 0.021 1.05e-02 9.07e+03 4.16e+00 bond pdb=" CA LEU E 345 " pdb=" C LEU E 345 " ideal model delta sigma weight residual 1.523 1.496 0.027 1.34e-02 5.57e+03 4.12e+00 bond pdb=" CA PHE C 263 " pdb=" CB PHE C 263 " ideal model delta sigma weight residual 1.534 1.505 0.029 1.45e-02 4.76e+03 4.05e+00 ... (remaining 17664 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 23860 2.08 - 4.15: 251 4.15 - 6.23: 18 6.23 - 8.31: 3 8.31 - 10.39: 3 Bond angle restraints: 24135 Sorted by residual: angle pdb=" O3' U G 7 " pdb=" C3' U G 7 " pdb=" C2' U G 7 " ideal model delta sigma weight residual 113.70 107.74 5.96 1.50e+00 4.44e-01 1.58e+01 angle pdb=" C SER C 261 " pdb=" CA SER C 261 " pdb=" CB SER C 261 " ideal model delta sigma weight residual 110.98 106.39 4.59 1.18e+00 7.18e-01 1.52e+01 angle pdb=" N PRO C 262 " pdb=" CA PRO C 262 " pdb=" C PRO C 262 " ideal model delta sigma weight residual 111.14 116.25 -5.11 1.56e+00 4.11e-01 1.07e+01 angle pdb=" CA LEU D 345 " pdb=" CB LEU D 345 " pdb=" CG LEU D 345 " ideal model delta sigma weight residual 116.30 126.69 -10.39 3.50e+00 8.16e-02 8.80e+00 angle pdb=" O3' U G 15 " pdb=" C3' U G 15 " pdb=" C2' U G 15 " ideal model delta sigma weight residual 113.70 109.27 4.43 1.50e+00 4.44e-01 8.71e+00 ... (remaining 24130 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.09: 9382 21.09 - 42.18: 875 42.18 - 63.27: 259 63.27 - 84.36: 38 84.36 - 105.45: 20 Dihedral angle restraints: 10574 sinusoidal: 4490 harmonic: 6084 Sorted by residual: dihedral pdb=" CA THR A 192 " pdb=" C THR A 192 " pdb=" N TYR A 193 " pdb=" CA TYR A 193 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA THR D 192 " pdb=" C THR D 192 " pdb=" N TYR D 193 " pdb=" CA TYR D 193 " ideal model delta harmonic sigma weight residual 180.00 160.53 19.47 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA THR E 192 " pdb=" C THR E 192 " pdb=" N TYR E 193 " pdb=" CA TYR E 193 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 10571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2068 0.046 - 0.092: 471 0.092 - 0.138: 217 0.138 - 0.184: 39 0.184 - 0.230: 9 Chirality restraints: 2804 Sorted by residual: chirality pdb=" C3' U G 15 " pdb=" C4' U G 15 " pdb=" O3' U G 15 " pdb=" C2' U G 15 " both_signs ideal model delta sigma weight residual False -2.48 -2.71 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C3' U G 7 " pdb=" C4' U G 7 " pdb=" O3' U G 7 " pdb=" C2' U G 7 " both_signs ideal model delta sigma weight residual False -2.48 -2.70 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C2' A H 1 " pdb=" C3' A H 1 " pdb=" O2' A H 1 " pdb=" C1' A H 1 " both_signs ideal model delta sigma weight residual False -2.75 -2.56 -0.19 2.00e-01 2.50e+01 9.43e-01 ... (remaining 2801 not shown) Planarity restraints: 2986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 204 " 0.050 5.00e-02 4.00e+02 7.57e-02 9.16e+00 pdb=" N PRO F 205 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO F 205 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 205 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 269 " -0.028 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO B 270 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 345 " 0.007 2.00e-02 2.50e+03 1.50e-02 2.24e+00 pdb=" C LEU F 345 " -0.026 2.00e-02 2.50e+03 pdb=" O LEU F 345 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN F 346 " 0.009 2.00e-02 2.50e+03 ... (remaining 2983 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2005 2.75 - 3.29: 16400 3.29 - 3.83: 30887 3.83 - 4.36: 38106 4.36 - 4.90: 63296 Nonbonded interactions: 150694 Sorted by model distance: nonbonded pdb=" OH TYR A 193 " pdb=" OE2 GLU A 304 " model vdw 2.217 3.040 nonbonded pdb=" O HIS D 242 " pdb=" OG SER D 287 " model vdw 2.223 3.040 nonbonded pdb=" O HIS E 242 " pdb=" OG SER E 287 " model vdw 2.245 3.040 nonbonded pdb=" O HIS C 242 " pdb=" OG SER C 287 " model vdw 2.245 3.040 nonbonded pdb=" NH1 ARG E 198 " pdb=" OE1 GLU E 210 " model vdw 2.251 3.120 ... (remaining 150689 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'B' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'C' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'D' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'E' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'F' and (resid 1 through 26 or resid 30 through 346)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.48 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.640 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17669 Z= 0.150 Angle : 0.529 10.385 24135 Z= 0.304 Chirality : 0.050 0.230 2804 Planarity : 0.003 0.076 2986 Dihedral : 18.218 105.447 6650 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.65 % Allowed : 23.92 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.19), residues: 2094 helix: 0.52 (0.23), residues: 534 sheet: 0.53 (0.28), residues: 342 loop : 0.27 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 135 TYR 0.008 0.001 TYR F 342 PHE 0.018 0.001 PHE D 258 TRP 0.018 0.001 TRP A 332 HIS 0.013 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00284 (17669) covalent geometry : angle 0.52900 (24135) hydrogen bonds : bond 0.18610 ( 635) hydrogen bonds : angle 8.37318 ( 1728) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 0.620 Fit side-chains REVERT: E 16 ASP cc_start: 0.8143 (t0) cc_final: 0.7497 (t70) REVERT: E 188 GLN cc_start: 0.7816 (tp40) cc_final: 0.7324 (tm-30) REVERT: B 266 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7458 (tt0) REVERT: A 345 LEU cc_start: 0.5690 (OUTLIER) cc_final: 0.5008 (tt) REVERT: C 191 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7769 (mm-30) outliers start: 12 outliers final: 3 residues processed: 201 average time/residue: 0.6445 time to fit residues: 144.2732 Evaluate side-chains 182 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 177 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 328 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 163 ASN E 346 GLN A 337 HIS C 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.166145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.113565 restraints weight = 106736.799| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.99 r_work: 0.2800 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17669 Z= 0.228 Angle : 0.582 8.802 24135 Z= 0.305 Chirality : 0.049 0.189 2804 Planarity : 0.004 0.062 2986 Dihedral : 10.400 83.674 2693 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.90 % Allowed : 22.04 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.19), residues: 2094 helix: 0.35 (0.22), residues: 540 sheet: 0.57 (0.28), residues: 354 loop : 0.20 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 126 TYR 0.015 0.002 TYR E 225 PHE 0.015 0.002 PHE C 329 TRP 0.009 0.002 TRP B 332 HIS 0.010 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00547 (17669) covalent geometry : angle 0.58217 (24135) hydrogen bonds : bond 0.04643 ( 635) hydrogen bonds : angle 6.10264 ( 1728) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 188 time to evaluate : 0.588 Fit side-chains REVERT: F 103 SER cc_start: 0.8816 (OUTLIER) cc_final: 0.8458 (p) REVERT: F 113 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7676 (mt-10) REVERT: F 136 ASN cc_start: 0.8001 (m110) cc_final: 0.7650 (m-40) REVERT: F 187 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7597 (mt0) REVERT: F 224 ARG cc_start: 0.7413 (ttm170) cc_final: 0.7171 (ttm-80) REVERT: F 228 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6621 (mp0) REVERT: D 21 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7625 (mt-10) REVERT: E 21 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.7993 (mt-10) REVERT: E 257 ARG cc_start: 0.7450 (tpt170) cc_final: 0.7130 (tmt-80) REVERT: E 264 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7462 (mm-30) REVERT: E 346 GLN cc_start: 0.4765 (OUTLIER) cc_final: 0.4554 (tp40) REVERT: B 345 LEU cc_start: 0.5906 (OUTLIER) cc_final: 0.5661 (pp) REVERT: A 345 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.5841 (tt) REVERT: C 110 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8666 (mtmt) REVERT: C 191 GLU cc_start: 0.8256 (mm-30) cc_final: 0.8012 (mm-30) outliers start: 52 outliers final: 14 residues processed: 224 average time/residue: 0.6718 time to fit residues: 167.0546 Evaluate side-chains 201 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 339 GLU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 147 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 80 optimal weight: 0.7980 chunk 138 optimal weight: 0.4980 chunk 135 optimal weight: 6.9990 chunk 204 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 198 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 277 ASN A 337 HIS C 14 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.168336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.115824 restraints weight = 104176.287| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.70 r_work: 0.2845 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17669 Z= 0.137 Angle : 0.507 9.127 24135 Z= 0.266 Chirality : 0.046 0.174 2804 Planarity : 0.003 0.052 2986 Dihedral : 9.621 81.705 2687 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.47 % Allowed : 22.31 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.19), residues: 2094 helix: 0.52 (0.23), residues: 540 sheet: 0.71 (0.29), residues: 324 loop : 0.19 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 138 TYR 0.010 0.001 TYR F 225 PHE 0.013 0.001 PHE E 263 TRP 0.009 0.001 TRP D 332 HIS 0.009 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00320 (17669) covalent geometry : angle 0.50661 (24135) hydrogen bonds : bond 0.03855 ( 635) hydrogen bonds : angle 5.55076 ( 1728) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 197 time to evaluate : 0.698 Fit side-chains REVERT: F 21 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: F 136 ASN cc_start: 0.8016 (m110) cc_final: 0.7728 (m-40) REVERT: F 228 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6929 (mt-10) REVERT: D 21 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7612 (mt-10) REVERT: D 232 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.7175 (m-80) REVERT: D 245 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7356 (tt) REVERT: E 16 ASP cc_start: 0.8554 (t70) cc_final: 0.8179 (t70) REVERT: E 188 GLN cc_start: 0.8166 (tp40) cc_final: 0.7809 (tm-30) REVERT: E 257 ARG cc_start: 0.7502 (tpt170) cc_final: 0.7132 (tmt-80) REVERT: E 264 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7410 (mm-30) REVERT: B 264 GLU cc_start: 0.6881 (tm-30) cc_final: 0.6584 (tm-30) REVERT: B 284 GLN cc_start: 0.8231 (tp40) cc_final: 0.7986 (tp-100) REVERT: B 344 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6600 (tmtt) REVERT: B 345 LEU cc_start: 0.6101 (OUTLIER) cc_final: 0.5754 (pp) REVERT: A 19 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8560 (mp-120) REVERT: A 264 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7562 (mt-10) REVERT: A 345 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.5699 (tt) REVERT: C 12 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8035 (mttt) REVERT: C 110 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8662 (mtmt) REVERT: C 191 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7867 (mm-30) REVERT: C 306 ILE cc_start: 0.6717 (tt) cc_final: 0.6104 (pt) outliers start: 44 outliers final: 14 residues processed: 227 average time/residue: 0.6338 time to fit residues: 160.9658 Evaluate side-chains 202 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 110 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 183 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 154 optimal weight: 0.4980 chunk 119 optimal weight: 3.9990 chunk 21 optimal weight: 0.3980 chunk 120 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.166514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.113725 restraints weight = 100775.225| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.68 r_work: 0.2813 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17669 Z= 0.195 Angle : 0.548 10.625 24135 Z= 0.285 Chirality : 0.048 0.188 2804 Planarity : 0.004 0.046 2986 Dihedral : 9.588 80.828 2686 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.12 % Allowed : 21.94 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.19), residues: 2094 helix: 0.47 (0.23), residues: 534 sheet: 0.67 (0.28), residues: 354 loop : 0.09 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 138 TYR 0.013 0.001 TYR E 225 PHE 0.013 0.002 PHE E 268 TRP 0.008 0.001 TRP B 332 HIS 0.003 0.001 HIS B 337 Details of bonding type rmsd covalent geometry : bond 0.00468 (17669) covalent geometry : angle 0.54797 (24135) hydrogen bonds : bond 0.04169 ( 635) hydrogen bonds : angle 5.63909 ( 1728) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 184 time to evaluate : 0.643 Fit side-chains REVERT: F 21 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8163 (mt-10) REVERT: F 136 ASN cc_start: 0.8061 (m110) cc_final: 0.7739 (m-40) REVERT: F 204 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7188 (mmtt) REVERT: F 224 ARG cc_start: 0.7385 (ttm170) cc_final: 0.6870 (ttm-80) REVERT: F 232 PHE cc_start: 0.7362 (m-80) cc_final: 0.6995 (m-80) REVERT: F 345 LEU cc_start: 0.4432 (OUTLIER) cc_final: 0.3438 (mt) REVERT: D 21 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7611 (mt-10) REVERT: D 199 ASN cc_start: 0.7673 (m-40) cc_final: 0.7330 (m110) REVERT: D 232 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.7120 (m-80) REVERT: D 245 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7418 (tt) REVERT: E 21 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.7979 (mt-10) REVERT: E 257 ARG cc_start: 0.7489 (tpt170) cc_final: 0.7154 (tmt-80) REVERT: E 264 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7350 (mm-30) REVERT: B 264 GLU cc_start: 0.6878 (tm-30) cc_final: 0.6605 (tm-30) REVERT: B 344 LYS cc_start: 0.7049 (OUTLIER) cc_final: 0.6753 (tmtt) REVERT: B 345 LEU cc_start: 0.5926 (OUTLIER) cc_final: 0.5539 (pp) REVERT: A 138 ARG cc_start: 0.8403 (ttt90) cc_final: 0.8189 (ttt90) REVERT: A 264 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7594 (mt-10) REVERT: A 284 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7098 (tm-30) REVERT: A 345 LEU cc_start: 0.6544 (OUTLIER) cc_final: 0.5823 (tt) REVERT: A 346 GLN cc_start: 0.5475 (OUTLIER) cc_final: 0.4314 (tm-30) REVERT: C 12 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8075 (mttt) REVERT: C 110 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8681 (mtmt) REVERT: C 191 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7889 (mm-30) outliers start: 54 outliers final: 15 residues processed: 224 average time/residue: 0.6534 time to fit residues: 163.6088 Evaluate side-chains 208 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 204 LYS Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 147 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 4.9990 chunk 70 optimal weight: 0.0970 chunk 83 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 133 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.168543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.127588 restraints weight = 101789.369| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 4.72 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17669 Z= 0.124 Angle : 0.492 9.756 24135 Z= 0.257 Chirality : 0.045 0.177 2804 Planarity : 0.003 0.042 2986 Dihedral : 9.351 78.601 2686 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.31 % Allowed : 22.85 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.19), residues: 2094 helix: 0.59 (0.23), residues: 540 sheet: 0.70 (0.28), residues: 354 loop : 0.15 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 138 TYR 0.010 0.001 TYR F 225 PHE 0.011 0.001 PHE E 268 TRP 0.006 0.001 TRP B 332 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd covalent geometry : bond 0.00288 (17669) covalent geometry : angle 0.49174 (24135) hydrogen bonds : bond 0.03610 ( 635) hydrogen bonds : angle 5.28931 ( 1728) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 0.707 Fit side-chains REVERT: F 21 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7676 (mt-10) REVERT: F 136 ASN cc_start: 0.7848 (m110) cc_final: 0.7579 (m-40) REVERT: F 204 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7267 (mmtm) REVERT: F 232 PHE cc_start: 0.7652 (m-80) cc_final: 0.7255 (m-80) REVERT: D 21 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7070 (mt-10) REVERT: D 187 GLN cc_start: 0.7267 (mm-40) cc_final: 0.7031 (mm-40) REVERT: D 199 ASN cc_start: 0.7350 (m-40) cc_final: 0.7145 (m110) REVERT: D 232 PHE cc_start: 0.7621 (OUTLIER) cc_final: 0.7385 (m-80) REVERT: D 245 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7274 (tt) REVERT: D 330 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6227 (mpp) REVERT: E 257 ARG cc_start: 0.7732 (tpt170) cc_final: 0.7427 (tmt-80) REVERT: E 264 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7022 (mm-30) REVERT: B 199 ASN cc_start: 0.7279 (m-40) cc_final: 0.6849 (t0) REVERT: B 264 GLU cc_start: 0.6670 (tm-30) cc_final: 0.6388 (tm-30) REVERT: B 266 GLU cc_start: 0.7644 (tt0) cc_final: 0.7166 (tt0) REVERT: B 344 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6849 (tmtt) REVERT: B 345 LEU cc_start: 0.5994 (OUTLIER) cc_final: 0.5626 (pp) REVERT: A 19 GLN cc_start: 0.8373 (mm-40) cc_final: 0.8101 (mp10) REVERT: A 56 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7343 (tt0) REVERT: A 138 ARG cc_start: 0.7993 (ttt90) cc_final: 0.7729 (ttt90) REVERT: A 232 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.7013 (t80) REVERT: A 264 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7156 (mt-10) REVERT: C 12 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7798 (mttt) REVERT: C 110 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8418 (mtmt) REVERT: C 191 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7528 (mm-30) outliers start: 38 outliers final: 14 residues processed: 216 average time/residue: 0.6636 time to fit residues: 160.0932 Evaluate side-chains 207 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 204 LYS Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 147 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 60 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.166404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.113605 restraints weight = 110637.428| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 4.11 r_work: 0.2781 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17669 Z= 0.196 Angle : 0.537 9.143 24135 Z= 0.281 Chirality : 0.048 0.194 2804 Planarity : 0.004 0.040 2986 Dihedral : 9.397 78.403 2684 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.85 % Allowed : 22.53 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.19), residues: 2094 helix: 0.50 (0.23), residues: 534 sheet: 0.86 (0.29), residues: 342 loop : 0.07 (0.19), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 138 TYR 0.012 0.001 TYR F 225 PHE 0.018 0.002 PHE E 221 TRP 0.008 0.001 TRP B 332 HIS 0.003 0.001 HIS B 337 Details of bonding type rmsd covalent geometry : bond 0.00471 (17669) covalent geometry : angle 0.53689 (24135) hydrogen bonds : bond 0.04072 ( 635) hydrogen bonds : angle 5.52544 ( 1728) *********************** 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 230 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 0.513 Fit side-chains REVERT: F 21 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8174 (mt-10) REVERT: F 34 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8413 (ttpp) REVERT: F 136 ASN cc_start: 0.8053 (m110) cc_final: 0.7752 (m-40) REVERT: F 204 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.7186 (mmtt) REVERT: F 224 ARG cc_start: 0.7371 (ttm170) cc_final: 0.6758 (ttm-80) REVERT: F 345 LEU cc_start: 0.4437 (OUTLIER) cc_final: 0.3512 (mt) REVERT: D 21 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7623 (mt-10) REVERT: D 199 ASN cc_start: 0.7636 (m-40) cc_final: 0.7388 (m110) REVERT: D 232 PHE cc_start: 0.7438 (OUTLIER) cc_final: 0.7137 (m-80) REVERT: D 245 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7403 (tt) REVERT: D 330 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.6205 (mpp) REVERT: E 257 ARG cc_start: 0.7469 (tpt170) cc_final: 0.7145 (tmt-80) REVERT: E 264 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7351 (mm-30) REVERT: B 264 GLU cc_start: 0.6849 (tm-30) cc_final: 0.6585 (tm-30) REVERT: B 344 LYS cc_start: 0.7050 (OUTLIER) cc_final: 0.6749 (tmtt) REVERT: B 345 LEU cc_start: 0.5576 (OUTLIER) cc_final: 0.5202 (pp) REVERT: A 138 ARG cc_start: 0.8379 (ttt90) cc_final: 0.8175 (ttt90) REVERT: A 264 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7601 (mt-10) REVERT: A 284 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.6990 (tm-30) REVERT: C 12 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8086 (mttt) REVERT: C 110 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8663 (mtmt) REVERT: C 191 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7838 (mm-30) outliers start: 45 outliers final: 20 residues processed: 214 average time/residue: 0.6447 time to fit residues: 153.8726 Evaluate side-chains 215 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 204 LYS Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 147 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 172 optimal weight: 0.9990 chunk 39 optimal weight: 0.0870 chunk 154 optimal weight: 0.0070 chunk 44 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 120 optimal weight: 0.4980 chunk 188 optimal weight: 0.9980 chunk 189 optimal weight: 0.7980 chunk 95 optimal weight: 0.0670 chunk 57 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.2914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.170663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131109 restraints weight = 104315.561| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 5.81 r_work: 0.2809 rms_B_bonded: 5.24 restraints_weight: 2.0000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17669 Z= 0.092 Angle : 0.465 9.051 24135 Z= 0.244 Chirality : 0.044 0.171 2804 Planarity : 0.003 0.036 2986 Dihedral : 9.121 76.108 2684 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.77 % Allowed : 23.82 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.19), residues: 2094 helix: 0.72 (0.23), residues: 540 sheet: 0.83 (0.29), residues: 324 loop : 0.15 (0.19), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 138 TYR 0.008 0.001 TYR C 225 PHE 0.022 0.001 PHE E 221 TRP 0.006 0.001 TRP D 86 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd covalent geometry : bond 0.00202 (17669) covalent geometry : angle 0.46543 (24135) hydrogen bonds : bond 0.03218 ( 635) hydrogen bonds : angle 4.99170 ( 1728) *********************** 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 225 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 0.504 Fit side-chains REVERT: F 136 ASN cc_start: 0.7999 (m110) cc_final: 0.7681 (m-40) REVERT: D 187 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7415 (mm-40) REVERT: D 216 LEU cc_start: 0.7445 (mt) cc_final: 0.7204 (mp) REVERT: D 232 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.7136 (m-80) REVERT: D 330 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.6014 (mpp) REVERT: E 257 ARG cc_start: 0.7378 (tpt170) cc_final: 0.6999 (tmt-80) REVERT: E 264 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7369 (mm-30) REVERT: B 34 LYS cc_start: 0.8697 (ttpt) cc_final: 0.8195 (ttmt) REVERT: B 138 ARG cc_start: 0.8394 (ttp-170) cc_final: 0.7597 (ttt90) REVERT: B 199 ASN cc_start: 0.7737 (m-40) cc_final: 0.7149 (t0) REVERT: B 218 MET cc_start: 0.7250 (ttp) cc_final: 0.7030 (ttm) REVERT: B 264 GLU cc_start: 0.6831 (tm-30) cc_final: 0.6526 (tm-30) REVERT: B 266 GLU cc_start: 0.7808 (tt0) cc_final: 0.7267 (tt0) REVERT: B 344 LYS cc_start: 0.6838 (OUTLIER) cc_final: 0.6514 (tmtt) REVERT: B 345 LEU cc_start: 0.5766 (OUTLIER) cc_final: 0.5391 (pp) REVERT: A 138 ARG cc_start: 0.8319 (ttt90) cc_final: 0.8086 (ttt90) REVERT: A 220 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7248 (tp30) REVERT: A 264 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7567 (mt-10) outliers start: 26 outliers final: 9 residues processed: 217 average time/residue: 0.5599 time to fit residues: 136.7855 Evaluate side-chains 201 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 340 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 170 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 164 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 180 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.167791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.127847 restraints weight = 101156.239| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 5.78 r_work: 0.2749 rms_B_bonded: 5.13 restraints_weight: 2.0000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17669 Z= 0.158 Angle : 0.508 8.696 24135 Z= 0.265 Chirality : 0.046 0.183 2804 Planarity : 0.003 0.036 2986 Dihedral : 9.164 74.954 2684 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.15 % Allowed : 23.49 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.19), residues: 2094 helix: 0.64 (0.23), residues: 540 sheet: 0.92 (0.29), residues: 342 loop : 0.14 (0.19), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 138 TYR 0.010 0.001 TYR C 225 PHE 0.028 0.002 PHE E 221 TRP 0.007 0.001 TRP A 332 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd covalent geometry : bond 0.00377 (17669) covalent geometry : angle 0.50786 (24135) hydrogen bonds : bond 0.03697 ( 635) hydrogen bonds : angle 5.26873 ( 1728) *********************** 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 217 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.693 Fit side-chains REVERT: F 34 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8295 (ttpp) REVERT: F 136 ASN cc_start: 0.8003 (m110) cc_final: 0.7709 (m-40) REVERT: F 345 LEU cc_start: 0.4350 (OUTLIER) cc_final: 0.3424 (mt) REVERT: D 187 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7454 (mm-40) REVERT: D 199 ASN cc_start: 0.7535 (m-40) cc_final: 0.7297 (m110) REVERT: D 232 PHE cc_start: 0.7380 (OUTLIER) cc_final: 0.7127 (m-80) REVERT: D 245 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7282 (tt) REVERT: D 330 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.6059 (mpp) REVERT: E 257 ARG cc_start: 0.7399 (tpt170) cc_final: 0.7092 (tmt-80) REVERT: E 264 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7410 (mm-30) REVERT: B 34 LYS cc_start: 0.8781 (ttpt) cc_final: 0.8266 (ttmt) REVERT: B 138 ARG cc_start: 0.8416 (ttp-170) cc_final: 0.7619 (ttt90) REVERT: B 199 ASN cc_start: 0.7911 (m-40) cc_final: 0.7334 (t0) REVERT: B 218 MET cc_start: 0.7224 (ttp) cc_final: 0.7013 (ttm) REVERT: B 264 GLU cc_start: 0.6844 (tm-30) cc_final: 0.6522 (tm-30) REVERT: B 345 LEU cc_start: 0.5433 (OUTLIER) cc_final: 0.5166 (pp) REVERT: A 138 ARG cc_start: 0.8337 (ttt90) cc_final: 0.8135 (ttt90) REVERT: A 232 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7061 (t80) REVERT: A 264 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7550 (mt-10) REVERT: A 345 LEU cc_start: 0.6139 (OUTLIER) cc_final: 0.5491 (tt) REVERT: C 12 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8063 (mtpt) outliers start: 32 outliers final: 13 residues processed: 208 average time/residue: 0.6321 time to fit residues: 147.2065 Evaluate side-chains 201 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 200 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 33 optimal weight: 8.9990 chunk 155 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 201 optimal weight: 0.9980 chunk 41 optimal weight: 0.0870 chunk 89 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.168837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.129220 restraints weight = 102547.811| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 5.78 r_work: 0.2764 rms_B_bonded: 5.18 restraints_weight: 2.0000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2733 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17669 Z= 0.126 Angle : 0.485 8.990 24135 Z= 0.254 Chirality : 0.045 0.188 2804 Planarity : 0.003 0.034 2986 Dihedral : 8.980 72.690 2684 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.99 % Allowed : 23.71 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.19), residues: 2094 helix: 0.69 (0.23), residues: 540 sheet: 0.90 (0.28), residues: 342 loop : 0.17 (0.19), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 138 TYR 0.011 0.001 TYR C 225 PHE 0.029 0.001 PHE E 221 TRP 0.005 0.001 TRP B 332 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd covalent geometry : bond 0.00295 (17669) covalent geometry : angle 0.48504 (24135) hydrogen bonds : bond 0.03441 ( 635) hydrogen bonds : angle 5.14351 ( 1728) *********************** 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 222 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.688 Fit side-chains REVERT: F 34 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8002 (tptm) REVERT: F 136 ASN cc_start: 0.7988 (m110) cc_final: 0.7690 (m-40) REVERT: F 345 LEU cc_start: 0.4410 (OUTLIER) cc_final: 0.3485 (mt) REVERT: D 21 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7591 (mt-10) REVERT: D 187 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7430 (mm-40) REVERT: D 199 ASN cc_start: 0.7467 (m-40) cc_final: 0.7243 (m110) REVERT: D 216 LEU cc_start: 0.7522 (mt) cc_final: 0.7270 (mp) REVERT: D 232 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.7138 (m-80) REVERT: D 245 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7249 (tt) REVERT: D 330 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.6070 (mpp) REVERT: E 264 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7390 (mm-30) REVERT: E 330 MET cc_start: 0.7142 (mmm) cc_final: 0.6341 (mmt) REVERT: B 34 LYS cc_start: 0.8763 (ttpt) cc_final: 0.8257 (ttmt) REVERT: B 138 ARG cc_start: 0.8401 (ttp-170) cc_final: 0.7610 (ttt90) REVERT: B 199 ASN cc_start: 0.7748 (m-40) cc_final: 0.7179 (t0) REVERT: B 264 GLU cc_start: 0.6766 (tm-30) cc_final: 0.6471 (tm-30) REVERT: B 266 GLU cc_start: 0.7842 (tt0) cc_final: 0.7312 (tt0) REVERT: B 284 GLN cc_start: 0.8193 (tp40) cc_final: 0.7944 (tp-100) REVERT: B 345 LEU cc_start: 0.5534 (OUTLIER) cc_final: 0.5283 (pp) REVERT: A 56 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8548 (tt0) REVERT: A 138 ARG cc_start: 0.8320 (ttt90) cc_final: 0.8113 (ttt90) REVERT: A 264 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7604 (mt-10) REVERT: A 345 LEU cc_start: 0.6062 (OUTLIER) cc_final: 0.5465 (tt) outliers start: 29 outliers final: 13 residues processed: 213 average time/residue: 0.6208 time to fit residues: 148.2314 Evaluate side-chains 211 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 147 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 179 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 195 optimal weight: 0.3980 chunk 167 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 166 optimal weight: 0.0980 chunk 176 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 173 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.168373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.128790 restraints weight = 116073.196| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 5.88 r_work: 0.2755 rms_B_bonded: 5.26 restraints_weight: 2.0000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17669 Z= 0.132 Angle : 0.489 8.868 24135 Z= 0.257 Chirality : 0.045 0.192 2804 Planarity : 0.003 0.034 2986 Dihedral : 8.854 70.339 2684 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.99 % Allowed : 23.71 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.19), residues: 2094 helix: 0.68 (0.23), residues: 540 sheet: 0.92 (0.28), residues: 342 loop : 0.16 (0.19), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 138 TYR 0.012 0.001 TYR F 225 PHE 0.030 0.002 PHE E 221 TRP 0.006 0.001 TRP A 332 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd covalent geometry : bond 0.00311 (17669) covalent geometry : angle 0.48881 (24135) hydrogen bonds : bond 0.03472 ( 635) hydrogen bonds : angle 5.16423 ( 1728) ********************** 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 220 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.634 Fit side-chains REVERT: F 34 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8296 (ttpp) REVERT: F 136 ASN cc_start: 0.7995 (m110) cc_final: 0.7698 (m-40) REVERT: F 224 ARG cc_start: 0.7275 (ttm170) cc_final: 0.7044 (ttm-80) REVERT: F 345 LEU cc_start: 0.4414 (OUTLIER) cc_final: 0.3481 (mt) REVERT: D 21 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7591 (mt-10) REVERT: D 187 GLN cc_start: 0.7788 (mm-40) cc_final: 0.7420 (mm-40) REVERT: D 199 ASN cc_start: 0.7493 (m-40) cc_final: 0.7266 (m110) REVERT: D 232 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.7146 (m-80) REVERT: D 245 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7266 (tt) REVERT: D 330 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.6089 (mpp) REVERT: E 56 GLU cc_start: 0.8828 (tt0) cc_final: 0.8509 (tt0) REVERT: E 264 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7412 (mm-30) REVERT: E 330 MET cc_start: 0.7164 (mmm) cc_final: 0.6356 (mmt) REVERT: B 34 LYS cc_start: 0.8775 (ttpt) cc_final: 0.8262 (ttmt) REVERT: B 138 ARG cc_start: 0.8424 (ttp-170) cc_final: 0.7622 (ttt90) REVERT: B 199 ASN cc_start: 0.7888 (m-40) cc_final: 0.7291 (t0) REVERT: B 264 GLU cc_start: 0.6829 (tm-30) cc_final: 0.6523 (tm-30) REVERT: B 266 GLU cc_start: 0.7802 (tt0) cc_final: 0.7273 (tt0) REVERT: B 284 GLN cc_start: 0.8202 (tp40) cc_final: 0.7946 (tp-100) REVERT: B 344 LYS cc_start: 0.6955 (OUTLIER) cc_final: 0.6630 (tmtt) REVERT: B 345 LEU cc_start: 0.5461 (OUTLIER) cc_final: 0.5258 (pp) REVERT: A 56 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8549 (tt0) REVERT: A 138 ARG cc_start: 0.8303 (ttt90) cc_final: 0.8098 (ttt90) REVERT: A 264 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7622 (mt-10) REVERT: A 345 LEU cc_start: 0.6082 (OUTLIER) cc_final: 0.5489 (tt) outliers start: 29 outliers final: 17 residues processed: 210 average time/residue: 0.6477 time to fit residues: 152.3536 Evaluate side-chains 212 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 147 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 23 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 0.0270 chunk 165 optimal weight: 0.9990 chunk 196 optimal weight: 0.0040 chunk 72 optimal weight: 1.9990 overall best weight: 0.4452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.167880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.115985 restraints weight = 107150.512| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.86 r_work: 0.2848 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17669 Z= 0.104 Angle : 0.469 9.189 24135 Z= 0.246 Chirality : 0.045 0.188 2804 Planarity : 0.003 0.033 2986 Dihedral : 8.625 65.887 2684 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.77 % Allowed : 23.92 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.19), residues: 2094 helix: 0.79 (0.23), residues: 540 sheet: 0.95 (0.28), residues: 342 loop : 0.21 (0.19), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 138 TYR 0.010 0.001 TYR C 225 PHE 0.027 0.001 PHE E 221 TRP 0.006 0.001 TRP D 332 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd covalent geometry : bond 0.00240 (17669) covalent geometry : angle 0.46942 (24135) hydrogen bonds : bond 0.03187 ( 635) hydrogen bonds : angle 4.98839 ( 1728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6294.70 seconds wall clock time: 108 minutes 21.63 seconds (6501.63 seconds total)