Starting phenix.real_space_refine on Sun Jun 15 10:00:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ud3_42145/06_2025/8ud3_42145.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ud3_42145/06_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_42145/06_2025/8ud3_42145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ud3_42145/06_2025/8ud3_42145.map" model { file = "/net/cci-nas-00/data/ceres_data/8ud3_42145/06_2025/8ud3_42145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ud3_42145/06_2025/8ud3_42145.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.046 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 19.87, per 1000 atoms: 1.15 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: 3.73 Conformation dependent library (CDL) restraints added in 4.4 seconds 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3924 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 47 sheets defined 26.8% alpha, 24.6% beta 15 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 6.32 Creating SS restraints... Processing helix chain 'F' and resid 1 through 13 Processing helix chain 'F' and resid 50 through 60 Processing helix chain 'F' and resid 68 through 75 Processing helix chain 'F' and resid 113 through 117 Processing helix chain 'F' and resid 129 through 137 Processing helix chain 'F' and resid 207 through 216 Processing helix chain 'F' and resid 217 through 225 Processing helix chain 'F' and resid 231 through 236 Processing helix chain 'F' and resid 250 through 261 removed outlier: 3.567A pdb=" N GLU F 260 " --> pdb=" O LYS F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 308 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 50 through 60 Processing helix chain 'D' and resid 68 through 75 Processing helix chain 'D' and resid 113 through 117 Processing helix chain 'D' and resid 129 through 137 Processing helix chain 'D' and resid 207 through 216 Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 231 through 236 removed outlier: 3.509A pdb=" N VAL D 236 " --> pdb=" O PHE D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.589A pdb=" N GLU D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 50 through 60 Processing helix chain 'E' and resid 68 through 75 Processing helix chain 'E' and resid 113 through 117 Processing helix chain 'E' and resid 129 through 136 Processing helix chain 'E' and resid 207 through 216 Processing helix chain 'E' and resid 217 through 225 Processing helix chain 'E' and resid 231 through 236 Processing helix chain 'E' and resid 250 through 261 removed outlier: 3.526A pdb=" N GLU E 260 " --> pdb=" O LYS E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 308 Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 50 through 60 Processing helix chain 'B' and resid 68 through 75 Processing helix chain 'B' and resid 113 through 117 Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 207 through 216 Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.550A pdb=" N GLU B 260 " --> pdb=" O LYS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 68 through 75 Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.665A pdb=" N GLU A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 308 Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 50 through 60 Processing helix chain 'C' and resid 68 through 75 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 129 through 136 Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.637A pdb=" N GLU C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 308 Processing sheet with id=AA1, first strand: chain 'F' and resid 24 through 27 removed outlier: 6.567A pdb=" N VAL F 31 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 79 through 80 removed outlier: 7.086A pdb=" N ILE F 79 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N ASP F 124 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LYS F 180 " --> pdb=" O GLN F 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'F' and resid 98 through 99 removed outlier: 8.036A pdb=" N THR F 98 " --> pdb=" O ILE F 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AA6, first strand: chain 'F' and resid 264 through 266 removed outlier: 4.958A pdb=" N ILE F 280 " --> pdb=" O CYS F 290 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N CYS F 290 " --> pdb=" O ILE F 280 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 315 through 322 removed outlier: 7.345A pdb=" N SER F 328 " --> pdb=" O PRO F 343 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N MET F 330 " --> pdb=" O PHE F 341 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE F 341 " --> pdb=" O MET F 330 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP F 332 " --> pdb=" O GLU F 339 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 24 through 27 removed outlier: 6.605A pdb=" N VAL D 31 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 79 through 80 removed outlier: 7.194A pdb=" N ILE D 79 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ASP D 124 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 79 through 80 removed outlier: 7.194A pdb=" N ILE D 79 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ASP D 124 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS D 180 " --> pdb=" O GLN D 187 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 86 through 87 Processing sheet with id=AB3, first strand: chain 'D' and resid 98 through 99 removed outlier: 8.016A pdb=" N THR D 98 " --> pdb=" O ILE D 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 160 through 162 Processing sheet with id=AB5, first strand: chain 'D' and resid 264 through 266 removed outlier: 4.949A pdb=" N ILE D 280 " --> pdb=" O CYS D 290 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N CYS D 290 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 315 through 322 removed outlier: 5.863A pdb=" N LYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL D 338 " --> pdb=" O LYS D 334 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 24 through 27 removed outlier: 6.594A pdb=" N VAL E 31 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.098A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N ASP E 124 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.098A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N ASP E 124 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LYS E 180 " --> pdb=" O GLN E 187 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AC2, first strand: chain 'E' and resid 98 through 99 removed outlier: 8.124A pdb=" N THR E 98 " --> pdb=" O ILE E 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 160 through 162 Processing sheet with id=AC4, first strand: chain 'E' and resid 264 through 266 removed outlier: 4.973A pdb=" N ILE E 280 " --> pdb=" O CYS E 290 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N CYS E 290 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 315 through 322 removed outlier: 7.154A pdb=" N SER E 328 " --> pdb=" O PRO E 343 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N MET E 330 " --> pdb=" O PHE E 341 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE E 341 " --> pdb=" O MET E 330 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP E 332 " --> pdb=" O GLU E 339 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 24 through 27 removed outlier: 6.634A pdb=" N VAL B 31 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.133A pdb=" N ILE B 79 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ASP B 124 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.133A pdb=" N ILE B 79 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ASP B 124 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LYS B 180 " --> pdb=" O GLN B 187 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AD1, first strand: chain 'B' and resid 98 through 99 removed outlier: 8.114A pdb=" N THR B 98 " --> pdb=" O ILE B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AD3, first strand: chain 'B' and resid 264 through 266 removed outlier: 4.935A pdb=" N ILE B 280 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N CYS B 290 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 315 through 322 removed outlier: 7.198A pdb=" N SER B 328 " --> pdb=" O PRO B 343 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N MET B 330 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE B 341 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP B 332 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 24 through 26 removed outlier: 6.651A pdb=" N VAL A 31 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.082A pdb=" N ILE A 79 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ASP A 124 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.082A pdb=" N ILE A 79 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ASP A 124 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS A 180 " --> pdb=" O GLN A 187 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AD9, first strand: chain 'A' and resid 98 through 99 removed outlier: 8.093A pdb=" N THR A 98 " --> pdb=" O ILE A 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AE2, first strand: chain 'A' and resid 264 through 266 removed outlier: 5.000A pdb=" N ILE A 280 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N CYS A 290 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 316 through 322 removed outlier: 3.956A pdb=" N TYR A 342 " --> pdb=" O MET A 330 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 24 through 26 removed outlier: 6.599A pdb=" N VAL C 31 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.129A pdb=" N ILE C 79 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N ASP C 124 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.129A pdb=" N ILE C 79 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N ASP C 124 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LYS C 180 " --> pdb=" O GLN C 187 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AE8, first strand: chain 'C' and resid 98 through 99 removed outlier: 8.042A pdb=" N THR C 98 " --> pdb=" O ILE C 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 160 through 162 Processing sheet with id=AF1, first strand: chain 'C' and resid 264 through 266 removed outlier: 4.792A pdb=" N ILE C 280 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N CYS C 290 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 315 through 322 removed outlier: 7.117A pdb=" N SER C 328 " --> pdb=" O PRO C 343 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N MET C 330 " --> pdb=" O PHE C 341 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE C 341 " --> pdb=" O MET C 330 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP C 332 " --> pdb=" O GLU C 339 " (cutoff:3.500A) 650 hydrogen bonds defined for protein. 1668 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 5.86 Time building geometry restraints manager: 4.49 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: 4.230 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: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 56.670 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.890 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (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 TRP 0.018 0.001 TRP A 332 HIS 0.013 0.001 HIS A 337 PHE 0.018 0.001 PHE D 258 TYR 0.008 0.001 TYR F 342 ARG 0.005 0.000 ARG E 135 Details of bonding type rmsd hydrogen bonds : bond 0.18610 ( 635) hydrogen bonds : angle 8.37318 ( 1728) covalent geometry : bond 0.00284 (17669) covalent geometry : angle 0.52900 (24135) *********************** 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 : 2.209 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: 0.5007 (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: 1.2763 time to fit residues: 287.0952 Evaluate side-chains 181 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 176 time to evaluate : 1.986 ------------------------------------------------------------------------------- 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 173 optimal weight: 0.2980 chunk 156 optimal weight: 0.0270 chunk 86 optimal weight: 0.0770 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 83 optimal weight: 0.2980 chunk 161 optimal weight: 0.0980 chunk 62 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 overall best weight: 0.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 HIS C 14 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.169739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.117560 restraints weight = 104678.059| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.79 r_work: 0.2895 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17669 Z= 0.094 Angle : 0.496 9.040 24135 Z= 0.260 Chirality : 0.045 0.165 2804 Planarity : 0.003 0.060 2986 Dihedral : 9.976 81.655 2693 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.20 % Allowed : 22.26 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.19), residues: 2094 helix: 0.79 (0.23), residues: 540 sheet: 0.93 (0.29), residues: 312 loop : 0.38 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 332 HIS 0.009 0.001 HIS A 337 PHE 0.009 0.001 PHE D 7 TYR 0.009 0.001 TYR F 225 ARG 0.005 0.000 ARG E 135 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 635) hydrogen bonds : angle 5.62511 ( 1728) covalent geometry : bond 0.00195 (17669) covalent geometry : angle 0.49628 (24135) *********************** 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 246 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 1.953 Fit side-chains REVERT: F 187 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7569 (mt0) REVERT: E 191 GLU cc_start: 0.7296 (tp30) cc_final: 0.6861 (tm-30) REVERT: E 199 ASN cc_start: 0.7876 (m-40) cc_final: 0.7231 (t0) REVERT: E 220 GLU cc_start: 0.6426 (OUTLIER) cc_final: 0.6083 (mp0) REVERT: E 241 SER cc_start: 0.8729 (m) cc_final: 0.8526 (m) REVERT: B 138 ARG cc_start: 0.8360 (ttp-170) cc_final: 0.7682 (ttt90) REVERT: B 264 GLU cc_start: 0.6841 (tm-30) cc_final: 0.6497 (tm-30) REVERT: B 345 LEU cc_start: 0.6005 (OUTLIER) cc_final: 0.5790 (pp) REVERT: A 19 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8564 (mp10) REVERT: A 264 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7531 (mt-10) REVERT: A 330 MET cc_start: 0.8280 (tpt) cc_final: 0.8077 (mmm) REVERT: A 345 LEU cc_start: 0.6390 (OUTLIER) cc_final: 0.5611 (tt) REVERT: C 138 ARG cc_start: 0.8243 (tpt-90) cc_final: 0.7357 (ttp-170) REVERT: C 191 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7857 (mm-30) REVERT: C 306 ILE cc_start: 0.6680 (tt) cc_final: 0.6099 (pt) outliers start: 41 outliers final: 7 residues processed: 234 average time/residue: 1.1357 time to fit residues: 300.9992 Evaluate side-chains 192 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 181 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 72 optimal weight: 1.9990 chunk 94 optimal weight: 0.1980 chunk 47 optimal weight: 2.9990 chunk 205 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 163 ASN D 277 ASN E 346 GLN A 337 HIS C 163 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.167317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.114830 restraints weight = 110734.030| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.86 r_work: 0.3078 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 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 : 0.008 0.058 17669 Z= 0.334 Angle : 0.653 11.425 24135 Z= 0.341 Chirality : 0.054 0.212 2804 Planarity : 0.004 0.055 2986 Dihedral : 9.968 82.710 2686 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.17 % Allowed : 21.94 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.18), residues: 2094 helix: 0.21 (0.22), residues: 534 sheet: 0.65 (0.28), residues: 354 loop : 0.07 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 332 HIS 0.010 0.002 HIS A 337 PHE 0.019 0.003 PHE B 15 TYR 0.017 0.002 TYR E 225 ARG 0.008 0.001 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.05107 ( 635) hydrogen bonds : angle 6.03824 ( 1728) covalent geometry : bond 0.00815 (17669) covalent geometry : angle 0.65325 (24135) *********************** 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 242 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 186 time to evaluate : 2.191 Fit side-chains REVERT: F 21 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8110 (mt-10) REVERT: F 34 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8515 (ttpp) REVERT: F 136 ASN cc_start: 0.8045 (m110) cc_final: 0.7788 (m-40) REVERT: F 187 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7546 (mt0) REVERT: F 204 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7268 (mmtm) REVERT: F 224 ARG cc_start: 0.7451 (ttm170) cc_final: 0.7179 (ttm-80) REVERT: F 277 ASN cc_start: 0.8898 (m-40) cc_final: 0.8679 (m-40) REVERT: D 21 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7613 (mt-10) REVERT: D 199 ASN cc_start: 0.7741 (m-40) cc_final: 0.7486 (m-40) REVERT: D 330 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.7199 (mmp) REVERT: E 16 ASP cc_start: 0.8576 (t70) cc_final: 0.8215 (t70) REVERT: E 21 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.7911 (mt-10) REVERT: B 344 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6898 (tmtt) REVERT: B 345 LEU cc_start: 0.5952 (OUTLIER) cc_final: 0.5622 (pp) REVERT: A 284 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7179 (tm-30) REVERT: A 345 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.5982 (tt) REVERT: A 346 GLN cc_start: 0.5603 (OUTLIER) cc_final: 0.4414 (tm-30) REVERT: C 110 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8649 (mtmt) REVERT: C 188 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8195 (tm-30) REVERT: C 191 GLU cc_start: 0.8248 (mm-30) cc_final: 0.8007 (mm-30) outliers start: 56 outliers final: 14 residues processed: 226 average time/residue: 1.3699 time to fit residues: 345.5569 Evaluate side-chains 203 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 1.762 ------------------------------------------------------------------------------- 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 103 SER Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 204 LYS Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 330 MET 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 B residue 91 ASP 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 214 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 345 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 183 optimal weight: 0.6980 chunk 147 optimal weight: 0.0370 chunk 205 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 86 optimal weight: 0.0000 chunk 97 optimal weight: 3.9990 chunk 21 optimal weight: 0.0670 chunk 156 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.3200 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.169978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131042 restraints weight = 94781.312| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 5.65 r_work: 0.2804 rms_B_bonded: 5.18 restraints_weight: 2.0000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 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 = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17669 Z= 0.097 Angle : 0.486 10.018 24135 Z= 0.254 Chirality : 0.045 0.149 2804 Planarity : 0.003 0.046 2986 Dihedral : 9.407 80.110 2686 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.67 % Allowed : 23.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.19), residues: 2094 helix: 0.56 (0.23), residues: 540 sheet: 0.83 (0.29), residues: 324 loop : 0.18 (0.19), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 332 HIS 0.004 0.001 HIS B 337 PHE 0.010 0.001 PHE E 268 TYR 0.008 0.001 TYR F 225 ARG 0.009 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 635) hydrogen bonds : angle 5.25824 ( 1728) covalent geometry : bond 0.00210 (17669) covalent geometry : angle 0.48578 (24135) *********************** 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 230 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 2.012 Fit side-chains REVERT: F 232 PHE cc_start: 0.7336 (OUTLIER) cc_final: 0.6917 (m-80) REVERT: D 21 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7608 (mt-10) REVERT: D 187 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7451 (mm-40) REVERT: D 199 ASN cc_start: 0.7446 (m-40) cc_final: 0.7195 (m110) REVERT: E 16 ASP cc_start: 0.8623 (t70) cc_final: 0.8407 (t70) REVERT: E 264 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7391 (mm-30) REVERT: B 264 GLU cc_start: 0.6905 (tm-30) cc_final: 0.6566 (tm-30) REVERT: B 284 GLN cc_start: 0.8173 (tp40) cc_final: 0.7914 (tp-100) REVERT: B 345 LEU cc_start: 0.5886 (OUTLIER) cc_final: 0.5663 (pp) REVERT: A 19 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8618 (mp10) REVERT: A 264 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7551 (mt-10) REVERT: A 345 LEU cc_start: 0.6179 (OUTLIER) cc_final: 0.5435 (tt) REVERT: C 191 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7888 (mm-30) REVERT: C 306 ILE cc_start: 0.6686 (tt) cc_final: 0.6097 (pt) outliers start: 29 outliers final: 5 residues processed: 224 average time/residue: 1.3592 time to fit residues: 344.0316 Evaluate side-chains 192 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 183 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 58 optimal weight: 4.9990 chunk 190 optimal weight: 0.1980 chunk 24 optimal weight: 5.9990 chunk 147 optimal weight: 0.0970 chunk 103 optimal weight: 0.4980 chunk 126 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.168167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.115880 restraints weight = 105303.010| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.89 r_work: 0.2871 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 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 = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1434 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= 0.142 Angle : 0.503 9.338 24135 Z= 0.262 Chirality : 0.046 0.182 2804 Planarity : 0.003 0.043 2986 Dihedral : 9.376 78.575 2686 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.83 % Allowed : 23.44 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.19), residues: 2094 helix: 0.62 (0.23), residues: 540 sheet: 0.87 (0.29), residues: 324 loop : 0.16 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 332 HIS 0.004 0.001 HIS B 337 PHE 0.022 0.002 PHE E 221 TYR 0.010 0.001 TYR C 225 ARG 0.007 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 635) hydrogen bonds : angle 5.32958 ( 1728) covalent geometry : bond 0.00335 (17669) covalent geometry : angle 0.50287 (24135) *********************** 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 223 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 1.819 Fit side-chains REVERT: F 136 ASN cc_start: 0.8039 (m110) cc_final: 0.7768 (m-40) REVERT: F 232 PHE cc_start: 0.7369 (m-80) cc_final: 0.6993 (m-80) REVERT: F 345 LEU cc_start: 0.4251 (OUTLIER) cc_final: 0.3409 (mt) REVERT: D 21 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7607 (mt-10) REVERT: D 187 GLN cc_start: 0.7821 (mm-40) cc_final: 0.7509 (mm-40) REVERT: D 199 ASN cc_start: 0.7519 (m-40) cc_final: 0.7160 (m110) REVERT: D 245 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7299 (tt) REVERT: D 330 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.7123 (mmp) REVERT: E 264 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7429 (mm-30) REVERT: B 264 GLU cc_start: 0.6867 (tm-30) cc_final: 0.6533 (tm-30) REVERT: B 284 GLN cc_start: 0.8203 (tp40) cc_final: 0.7923 (tp-100) REVERT: B 344 LYS cc_start: 0.6903 (OUTLIER) cc_final: 0.6609 (tmtt) REVERT: B 345 LEU cc_start: 0.5908 (OUTLIER) cc_final: 0.5569 (pp) REVERT: A 264 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7582 (mt-10) REVERT: A 345 LEU cc_start: 0.6289 (OUTLIER) cc_final: 0.5642 (tt) REVERT: C 188 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8033 (tm-30) REVERT: C 191 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7830 (mm-30) outliers start: 30 outliers final: 13 residues processed: 214 average time/residue: 1.1970 time to fit residues: 289.1421 Evaluate side-chains 211 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 96 ILE 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 152 GLN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 232 PHE 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 78 ASP Chi-restraints excluded: chain C residue 188 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 196 optimal weight: 0.0000 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 117 optimal weight: 0.0980 chunk 175 optimal weight: 0.7980 chunk 185 optimal weight: 0.5980 chunk 147 optimal weight: 0.0370 overall best weight: 0.2862 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.169090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.116945 restraints weight = 106458.644| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.99 r_work: 0.2898 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 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 = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1658 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= 0.089 Angle : 0.465 9.048 24135 Z= 0.242 Chirality : 0.044 0.170 2804 Planarity : 0.003 0.038 2986 Dihedral : 9.157 76.503 2686 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.56 % Allowed : 23.92 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.19), residues: 2094 helix: 0.77 (0.23), residues: 540 sheet: 0.93 (0.29), residues: 324 loop : 0.21 (0.19), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 332 HIS 0.004 0.001 HIS B 337 PHE 0.023 0.001 PHE E 221 TYR 0.010 0.001 TYR D 278 ARG 0.010 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.03165 ( 635) hydrogen bonds : angle 4.93379 ( 1728) covalent geometry : bond 0.00198 (17669) covalent geometry : angle 0.46466 (24135) *********************** 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 229 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 1.810 Fit side-chains REVERT: D 21 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7528 (mt-10) REVERT: D 187 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7393 (mm-40) REVERT: D 245 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7226 (tt) REVERT: D 330 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.7125 (mmp) REVERT: E 264 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7387 (mm-30) REVERT: B 34 LYS cc_start: 0.8655 (ttpt) cc_final: 0.8202 (ttmt) REVERT: B 138 ARG cc_start: 0.8327 (ttp-170) cc_final: 0.7600 (ttt90) REVERT: B 199 ASN cc_start: 0.7609 (m-40) cc_final: 0.7073 (t0) REVERT: B 264 GLU cc_start: 0.6790 (tm-30) cc_final: 0.6459 (tm-30) REVERT: B 345 LEU cc_start: 0.5848 (OUTLIER) cc_final: 0.5604 (pp) REVERT: A 19 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8541 (mp10) REVERT: A 220 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7274 (tp30) REVERT: A 264 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7471 (mt-10) REVERT: C 264 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7295 (mt-10) outliers start: 26 outliers final: 11 residues processed: 220 average time/residue: 1.1560 time to fit residues: 287.6046 Evaluate side-chains 202 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 1.836 ------------------------------------------------------------------------------- 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 21 GLU 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 B residue 47 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain C residue 12 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 78 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 196 optimal weight: 0.0570 chunk 7 optimal weight: 0.0370 chunk 42 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 26 optimal weight: 0.0670 overall best weight: 0.5916 ------------------------------------------------------------------------------- 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 = 0.4004 r_free = 0.4004 target = 0.176829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.139738 restraints weight = 112736.441| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 4.94 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1628 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= 0.122 Angle : 0.487 8.812 24135 Z= 0.252 Chirality : 0.045 0.172 2804 Planarity : 0.003 0.044 2986 Dihedral : 9.141 75.430 2684 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.94 % Allowed : 23.55 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.19), residues: 2094 helix: 0.77 (0.23), residues: 540 sheet: 1.14 (0.29), residues: 312 loop : 0.22 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 332 HIS 0.004 0.001 HIS B 337 PHE 0.028 0.001 PHE E 221 TYR 0.010 0.001 TYR D 278 ARG 0.009 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 635) hydrogen bonds : angle 5.07286 ( 1728) covalent geometry : bond 0.00285 (17669) covalent geometry : angle 0.48684 (24135) *********************** 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 223 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 1.717 Fit side-chains REVERT: D 21 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.6967 (mt-10) REVERT: D 245 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7424 (tt) REVERT: E 264 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7274 (mm-30) REVERT: B 34 LYS cc_start: 0.8206 (ttpt) cc_final: 0.7984 (ttmt) REVERT: B 56 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7428 (tt0) REVERT: B 138 ARG cc_start: 0.8016 (ttp-170) cc_final: 0.7682 (ttt90) REVERT: B 199 ASN cc_start: 0.7279 (m-40) cc_final: 0.7041 (t0) REVERT: B 264 GLU cc_start: 0.6807 (tm-30) cc_final: 0.6522 (tm-30) REVERT: B 345 LEU cc_start: 0.5815 (OUTLIER) cc_final: 0.5529 (pp) REVERT: A 264 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7218 (mt-10) outliers start: 32 outliers final: 15 residues processed: 213 average time/residue: 1.1727 time to fit residues: 281.8189 Evaluate side-chains 204 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 1.720 ------------------------------------------------------------------------------- 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 21 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 147 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 189 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 191 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 187 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.175592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.138048 restraints weight = 113293.458| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 4.96 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3584 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17669 Z= 0.147 Angle : 0.507 8.900 24135 Z= 0.264 Chirality : 0.046 0.188 2804 Planarity : 0.003 0.045 2986 Dihedral : 9.115 74.097 2684 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.88 % Allowed : 23.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.19), residues: 2094 helix: 0.69 (0.23), residues: 540 sheet: 1.05 (0.29), residues: 342 loop : 0.20 (0.19), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 332 HIS 0.004 0.001 HIS B 337 PHE 0.029 0.002 PHE E 221 TYR 0.011 0.001 TYR F 225 ARG 0.009 0.001 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 635) hydrogen bonds : angle 5.20930 ( 1728) covalent geometry : bond 0.00349 (17669) covalent geometry : angle 0.50675 (24135) *********************** 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 218 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 1.808 Fit side-chains REVERT: F 224 ARG cc_start: 0.7696 (ttm170) cc_final: 0.7481 (ttm-80) REVERT: F 232 PHE cc_start: 0.7633 (m-80) cc_final: 0.7303 (m-80) REVERT: F 345 LEU cc_start: 0.4158 (OUTLIER) cc_final: 0.3322 (mp) REVERT: D 21 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7000 (mt-10) REVERT: D 245 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7418 (tt) REVERT: E 264 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7267 (mm-30) REVERT: B 34 LYS cc_start: 0.8296 (ttpt) cc_final: 0.8039 (ttmt) REVERT: B 56 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: B 138 ARG cc_start: 0.8009 (ttp-170) cc_final: 0.7641 (ttt90) REVERT: B 199 ASN cc_start: 0.7342 (m-40) cc_final: 0.7089 (t0) REVERT: B 264 GLU cc_start: 0.6744 (tm-30) cc_final: 0.6476 (tm-30) REVERT: B 345 LEU cc_start: 0.5843 (OUTLIER) cc_final: 0.5564 (pp) REVERT: A 264 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7202 (mt-10) outliers start: 30 outliers final: 18 residues processed: 208 average time/residue: 1.2389 time to fit residues: 290.2137 Evaluate side-chains 206 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 245 LEU Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 147 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 0.0980 chunk 10 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 117 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4009 r_free = 0.4009 target = 0.177370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.139922 restraints weight = 116611.863| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 5.02 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1727 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= 0.110 Angle : 0.478 8.919 24135 Z= 0.249 Chirality : 0.045 0.183 2804 Planarity : 0.003 0.043 2986 Dihedral : 8.852 70.759 2684 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.67 % Allowed : 23.87 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.19), residues: 2094 helix: 0.75 (0.23), residues: 540 sheet: 1.16 (0.30), residues: 312 loop : 0.22 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 332 HIS 0.004 0.001 HIS B 337 PHE 0.028 0.001 PHE E 221 TYR 0.009 0.001 TYR C 225 ARG 0.009 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.03278 ( 635) hydrogen bonds : angle 5.01598 ( 1728) covalent geometry : bond 0.00256 (17669) covalent geometry : angle 0.47778 (24135) *********************** 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 215 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 1.930 Fit side-chains REVERT: F 232 PHE cc_start: 0.7609 (m-80) cc_final: 0.7327 (m-80) REVERT: D 21 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.6930 (mt-10) REVERT: D 245 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7405 (tt) REVERT: E 264 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7307 (mm-30) REVERT: B 34 LYS cc_start: 0.8250 (ttpt) cc_final: 0.8015 (ttmt) REVERT: B 56 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7413 (tt0) REVERT: B 138 ARG cc_start: 0.8018 (ttp-170) cc_final: 0.7649 (ttt90) REVERT: B 199 ASN cc_start: 0.7349 (m-40) cc_final: 0.7141 (t0) REVERT: B 264 GLU cc_start: 0.6846 (tm-30) cc_final: 0.6582 (tm-30) REVERT: B 345 LEU cc_start: 0.5737 (OUTLIER) cc_final: 0.5447 (pp) REVERT: A 220 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7448 (tp30) REVERT: A 260 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7079 (pm20) REVERT: A 264 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7119 (mt-10) outliers start: 26 outliers final: 17 residues processed: 205 average time/residue: 1.1881 time to fit residues: 273.8439 Evaluate side-chains 207 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 1.721 ------------------------------------------------------------------------------- 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 21 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain B residue 56 GLU 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 232 PHE Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 260 GLU 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 78 ASP 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 25 optimal weight: 0.3980 chunk 148 optimal weight: 0.2980 chunk 134 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 53 optimal weight: 0.0670 chunk 42 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 173 optimal weight: 0.4980 chunk 121 optimal weight: 1.9990 chunk 75 optimal weight: 0.1980 overall best weight: 0.2718 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.179843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.143156 restraints weight = 98869.283| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 4.76 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3641 r_free = 0.3641 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3641 r_free = 0.3641 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1911 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= 0.088 Angle : 0.460 9.208 24135 Z= 0.240 Chirality : 0.044 0.180 2804 Planarity : 0.003 0.040 2986 Dihedral : 8.532 65.250 2684 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.29 % Allowed : 24.57 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.19), residues: 2094 helix: 0.78 (0.23), residues: 546 sheet: 1.17 (0.29), residues: 312 loop : 0.30 (0.19), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 332 HIS 0.004 0.001 HIS B 337 PHE 0.027 0.001 PHE E 221 TYR 0.009 0.001 TYR D 278 ARG 0.009 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.02937 ( 635) hydrogen bonds : angle 4.77168 ( 1728) covalent geometry : bond 0.00197 (17669) covalent geometry : angle 0.46022 (24135) ********************** 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 216 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 1.994 Fit side-chains REVERT: F 149 LYS cc_start: 0.7871 (mtmm) cc_final: 0.7663 (pttm) REVERT: D 21 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.6906 (mm-30) REVERT: D 245 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7396 (tt) REVERT: E 264 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7216 (mm-30) REVERT: E 330 MET cc_start: 0.7210 (mmm) cc_final: 0.6650 (mmt) REVERT: B 34 LYS cc_start: 0.8207 (ttpt) cc_final: 0.7990 (ttmt) REVERT: B 138 ARG cc_start: 0.8025 (ttp-170) cc_final: 0.7655 (ttt90) REVERT: B 264 GLU cc_start: 0.6802 (tm-30) cc_final: 0.6542 (tm-30) REVERT: A 187 GLN cc_start: 0.7459 (mm110) cc_final: 0.7199 (mm-40) REVERT: A 264 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7162 (mt-10) REVERT: C 138 ARG cc_start: 0.7806 (mtp85) cc_final: 0.7203 (ttp-170) REVERT: C 208 GLN cc_start: 0.7598 (tp-100) cc_final: 0.7334 (tm-30) outliers start: 19 outliers final: 11 residues processed: 209 average time/residue: 1.3921 time to fit residues: 330.9810 Evaluate side-chains 195 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 2.324 ------------------------------------------------------------------------------- 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 21 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU 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 232 PHE Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 340 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 6 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 136 optimal weight: 0.0050 chunk 37 optimal weight: 0.0670 chunk 150 optimal weight: 0.0870 chunk 109 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 overall best weight: 0.2710 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.179777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.142857 restraints weight = 106588.595| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 5.05 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17669 Z= 0.088 Angle : 0.465 11.835 24135 Z= 0.241 Chirality : 0.044 0.187 2804 Planarity : 0.003 0.043 2986 Dihedral : 8.464 62.196 2684 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.97 % Allowed : 24.89 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.19), residues: 2094 helix: 0.83 (0.23), residues: 546 sheet: 1.19 (0.29), residues: 312 loop : 0.32 (0.19), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 332 HIS 0.004 0.001 HIS B 337 PHE 0.028 0.001 PHE E 221 TYR 0.009 0.001 TYR C 225 ARG 0.009 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.02926 ( 635) hydrogen bonds : angle 4.74241 ( 1728) covalent geometry : bond 0.00198 (17669) covalent geometry : angle 0.46460 (24135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11575.74 seconds wall clock time: 201 minutes 4.78 seconds (12064.78 seconds total)