Starting phenix.real_space_refine on Sun May 18 16:09:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ud3_42145/05_2025/8ud3_42145.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ud3_42145/05_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_42145/05_2025/8ud3_42145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ud3_42145/05_2025/8ud3_42145.map" model { file = "/net/cci-nas-00/data/ceres_data/8ud3_42145/05_2025/8ud3_42145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ud3_42145/05_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-5687/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: 17.06, per 1000 atoms: 0.99 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: 3.63 Conformation dependent library (CDL) restraints added in 3.7 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: 6.15 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: 5.95 Time building geometry restraints manager: 4.35 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: 3.140 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: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 51.330 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.110 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:11.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.120 ------------------------------------------------------------------------------- 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 : 1.848 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: 1.2677 time to fit residues: 285.1077 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 : 1.752 ------------------------------------------------------------------------------- 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 = 0.117557 restraints weight = 104678.052| |-----------------------------------------------------------------------------| 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: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 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 : 2.215 Fit side-chains REVERT: F 187 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7574 (mt0) REVERT: E 191 GLU cc_start: 0.7298 (tp30) cc_final: 0.6864 (tm-30) REVERT: E 199 ASN cc_start: 0.7877 (m-40) cc_final: 0.7233 (t0) REVERT: E 220 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.6091 (mp0) REVERT: E 241 SER cc_start: 0.8731 (m) cc_final: 0.8529 (m) REVERT: B 138 ARG cc_start: 0.8359 (ttp-170) cc_final: 0.7684 (ttt90) REVERT: B 264 GLU cc_start: 0.6845 (tm-30) cc_final: 0.6502 (tm-30) REVERT: B 345 LEU cc_start: 0.6004 (OUTLIER) cc_final: 0.5790 (pp) REVERT: A 19 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8568 (mp10) REVERT: A 264 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7536 (mt-10) REVERT: A 330 MET cc_start: 0.8276 (tpt) cc_final: 0.8074 (mmm) REVERT: A 345 LEU cc_start: 0.6391 (OUTLIER) cc_final: 0.5616 (tt) REVERT: C 138 ARG cc_start: 0.8246 (tpt-90) cc_final: 0.7361 (ttp-170) REVERT: C 191 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7861 (mm-30) REVERT: C 306 ILE cc_start: 0.6686 (tt) cc_final: 0.6106 (pt) outliers start: 41 outliers final: 7 residues processed: 234 average time/residue: 1.1349 time to fit residues: 301.3901 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 : 1.747 ------------------------------------------------------------------------------- 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: 0.3980 chunk 47 optimal weight: 2.9990 chunk 205 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.165741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.112184 restraints weight = 105731.279| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.93 r_work: 0.2859 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 17669 Z= 0.264 Angle : 0.596 11.276 24135 Z= 0.311 Chirality : 0.050 0.193 2804 Planarity : 0.004 0.055 2986 Dihedral : 9.836 81.927 2686 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.58 % Allowed : 22.63 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.19), residues: 2094 helix: 0.42 (0.22), residues: 534 sheet: 0.70 (0.28), residues: 354 loop : 0.15 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 332 HIS 0.010 0.001 HIS A 337 PHE 0.016 0.002 PHE C 329 TYR 0.015 0.002 TYR F 225 ARG 0.008 0.001 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.04686 ( 635) hydrogen bonds : angle 5.89489 ( 1728) covalent geometry : bond 0.00641 (17669) covalent geometry : angle 0.59642 (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 231 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 185 time to evaluate : 1.879 Fit side-chains REVERT: F 103 SER cc_start: 0.8861 (OUTLIER) cc_final: 0.8502 (p) REVERT: F 136 ASN cc_start: 0.8048 (m110) cc_final: 0.7764 (m-40) REVERT: F 187 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7593 (mt0) REVERT: F 224 ARG cc_start: 0.7437 (ttm170) cc_final: 0.6770 (ttm-80) REVERT: D 21 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7572 (mt-10) REVERT: D 232 PHE cc_start: 0.7477 (OUTLIER) cc_final: 0.7143 (m-80) REVERT: E 16 ASP cc_start: 0.8617 (t70) cc_final: 0.8217 (t70) REVERT: E 21 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8006 (mt-10) REVERT: E 264 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7403 (mm-30) REVERT: E 346 GLN cc_start: 0.4702 (OUTLIER) cc_final: 0.4494 (tp40) REVERT: B 264 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6601 (tm-30) REVERT: B 344 LYS cc_start: 0.7064 (OUTLIER) cc_final: 0.6773 (tmtt) REVERT: B 345 LEU cc_start: 0.5945 (OUTLIER) cc_final: 0.5606 (pp) REVERT: A 264 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7622 (mt-10) REVERT: A 284 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7169 (tm-30) REVERT: A 345 LEU cc_start: 0.6573 (OUTLIER) cc_final: 0.5846 (tt) REVERT: C 110 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8678 (mtmt) REVERT: C 188 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8094 (tm-30) REVERT: C 191 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7948 (mm-30) outliers start: 46 outliers final: 16 residues processed: 219 average time/residue: 1.3121 time to fit residues: 322.0237 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 : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain B residue 91 ASP 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 147 SER 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 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 C residue 12 LYS Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 147 SER 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: 1.9990 chunk 147 optimal weight: 0.0050 chunk 205 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 156 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.168055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.130371 restraints weight = 95577.376| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 5.48 r_work: 0.2772 rms_B_bonded: 5.19 restraints_weight: 2.0000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17669 Z= 0.117 Angle : 0.495 9.948 24135 Z= 0.258 Chirality : 0.045 0.163 2804 Planarity : 0.003 0.046 2986 Dihedral : 9.449 80.110 2686 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.77 % Allowed : 23.39 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.19), residues: 2094 helix: 0.63 (0.23), residues: 540 sheet: 0.84 (0.29), residues: 324 loop : 0.20 (0.18), 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 0.011 0.001 PHE E 268 TYR 0.009 0.001 TYR F 225 ARG 0.008 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.03582 ( 635) hydrogen bonds : angle 5.34176 ( 1728) covalent geometry : bond 0.00273 (17669) covalent geometry : angle 0.49483 (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 226 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 1.843 Fit side-chains REVERT: F 187 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7642 (mt0) REVERT: F 232 PHE cc_start: 0.7341 (m-80) cc_final: 0.6971 (m-80) REVERT: D 21 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7680 (mt-10) REVERT: D 187 GLN cc_start: 0.7816 (mm-40) cc_final: 0.7493 (mm-40) REVERT: D 199 ASN cc_start: 0.7464 (m-40) cc_final: 0.7213 (m110) REVERT: D 232 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.7077 (m-80) REVERT: D 245 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7288 (tt) REVERT: D 330 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.7184 (mmp) REVERT: E 264 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7434 (mm-30) REVERT: B 264 GLU cc_start: 0.6875 (tm-30) cc_final: 0.6569 (tm-30) REVERT: B 284 GLN cc_start: 0.8163 (tp40) cc_final: 0.7899 (tp-100) REVERT: B 345 LEU cc_start: 0.5877 (OUTLIER) cc_final: 0.5641 (pp) REVERT: A 19 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8604 (mp-120) REVERT: A 264 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7580 (mt-10) REVERT: A 345 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.5513 (tt) REVERT: C 110 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8646 (mtmt) REVERT: C 191 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7886 (mm-30) REVERT: C 306 ILE cc_start: 0.6698 (tt) cc_final: 0.6093 (pt) outliers start: 31 outliers final: 9 residues processed: 217 average time/residue: 1.2052 time to fit residues: 294.8690 Evaluate side-chains 197 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 110 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 58 optimal weight: 0.0070 chunk 190 optimal weight: 0.2980 chunk 24 optimal weight: 5.9990 chunk 147 optimal weight: 0.0770 chunk 103 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 202 optimal weight: 4.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.167431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.115354 restraints weight = 106536.017| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.89 r_work: 0.2829 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1505 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= 0.106 Angle : 0.477 9.377 24135 Z= 0.249 Chirality : 0.045 0.169 2804 Planarity : 0.003 0.042 2986 Dihedral : 9.263 77.011 2686 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.72 % Allowed : 23.82 % 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: 0.62 (0.19), residues: 2094 helix: 0.77 (0.23), residues: 540 sheet: 0.90 (0.29), residues: 324 loop : 0.22 (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 0.009 0.001 PHE A 268 TYR 0.009 0.001 TYR C 225 ARG 0.008 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 635) hydrogen bonds : angle 5.11069 ( 1728) covalent geometry : bond 0.00242 (17669) covalent geometry : angle 0.47701 (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 225 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 1.927 Fit side-chains REVERT: F 136 ASN cc_start: 0.7997 (m110) cc_final: 0.7716 (m-40) REVERT: F 187 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7562 (mt0) REVERT: F 232 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6953 (m-80) REVERT: D 21 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7568 (mt-10) REVERT: D 187 GLN cc_start: 0.7799 (mm-40) cc_final: 0.7447 (mm-40) REVERT: D 199 ASN cc_start: 0.7396 (m-40) cc_final: 0.7171 (m110) REVERT: D 232 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.7140 (m-80) REVERT: D 245 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7225 (tt) REVERT: E 264 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7366 (mm-30) REVERT: B 34 LYS cc_start: 0.8603 (ttpt) cc_final: 0.8140 (ttmt) REVERT: B 138 ARG cc_start: 0.8347 (ttp-170) cc_final: 0.7609 (ttt90) REVERT: B 199 ASN cc_start: 0.7453 (m-40) cc_final: 0.7021 (t0) REVERT: B 264 GLU cc_start: 0.6762 (tm-30) cc_final: 0.6430 (tm-30) REVERT: B 284 GLN cc_start: 0.8161 (tp40) cc_final: 0.7883 (tp-100) REVERT: B 344 LYS cc_start: 0.6762 (OUTLIER) cc_final: 0.6510 (tmtt) REVERT: B 345 LEU cc_start: 0.5903 (OUTLIER) cc_final: 0.5570 (pp) REVERT: A 19 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8533 (mp10) REVERT: A 264 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7467 (mt-10) REVERT: A 345 LEU cc_start: 0.6074 (OUTLIER) cc_final: 0.5417 (tt) REVERT: C 306 ILE cc_start: 0.6656 (tt) cc_final: 0.6081 (pt) outliers start: 30 outliers final: 9 residues processed: 216 average time/residue: 1.0743 time to fit residues: 264.1982 Evaluate side-chains 200 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain E residue 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 344 LYS Chi-restraints excluded: chain B residue 345 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 196 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 0.2980 chunk 20 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 117 optimal weight: 0.0670 chunk 175 optimal weight: 0.5980 chunk 185 optimal weight: 0.0980 chunk 147 optimal weight: 0.7980 overall best weight: 0.3318 ------------------------------------------------------------------------------- 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 = 0.3879 r_free = 0.3879 target = 0.171171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.119346 restraints weight = 105591.480| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.77 r_work: 0.2867 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1683 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= 0.093 Angle : 0.463 9.102 24135 Z= 0.241 Chirality : 0.044 0.168 2804 Planarity : 0.003 0.039 2986 Dihedral : 9.131 75.411 2686 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.56 % Allowed : 23.71 % 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: 0.68 (0.19), residues: 2094 helix: 0.85 (0.23), residues: 540 sheet: 0.97 (0.29), residues: 324 loop : 0.23 (0.19), residues: 1230 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 0.013 0.001 PHE E 221 TYR 0.008 0.001 TYR C 225 ARG 0.009 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.03156 ( 635) hydrogen bonds : angle 4.93434 ( 1728) covalent geometry : bond 0.00208 (17669) covalent geometry : angle 0.46263 (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 220 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 1.865 Fit side-chains revert: symmetry clash REVERT: F 232 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.6979 (m-80) REVERT: D 21 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7542 (mt-10) REVERT: D 187 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7403 (mm-40) REVERT: D 232 PHE cc_start: 0.7380 (OUTLIER) cc_final: 0.7095 (m-80) REVERT: E 191 GLU cc_start: 0.7268 (tp30) cc_final: 0.6821 (tm-30) REVERT: E 264 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7300 (mm-30) REVERT: E 330 MET cc_start: 0.7344 (mmm) cc_final: 0.6544 (mmt) REVERT: B 34 LYS cc_start: 0.8599 (ttpt) cc_final: 0.8144 (ttmt) REVERT: B 109 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8287 (mppt) REVERT: B 138 ARG cc_start: 0.8345 (ttp-170) cc_final: 0.7606 (ttt90) REVERT: B 199 ASN cc_start: 0.7577 (m-40) cc_final: 0.7075 (t0) REVERT: B 264 GLU cc_start: 0.6741 (tm-30) cc_final: 0.6402 (tm-30) REVERT: B 284 GLN cc_start: 0.8134 (tp40) cc_final: 0.7847 (tp-100) REVERT: B 345 LEU cc_start: 0.5643 (OUTLIER) cc_final: 0.5410 (pp) REVERT: A 19 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8508 (mp10) REVERT: A 220 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7216 (tp30) REVERT: A 264 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7462 (mt-10) outliers start: 27 outliers final: 10 residues processed: 211 average time/residue: 1.1179 time to fit residues: 267.2500 Evaluate side-chains 198 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 232 PHE 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 109 LYS 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 232 PHE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 340 THR 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: 4.9990 chunk 130 optimal weight: 2.9990 chunk 44 optimal weight: 0.0770 chunk 196 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 overall best weight: 0.6540 ------------------------------------------------------------------------------- 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 = 0.176764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.139276 restraints weight = 112728.543| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 4.99 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3596 r_free = 0.3596 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3596 r_free = 0.3596 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1624 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= 0.128 Angle : 0.487 8.938 24135 Z= 0.253 Chirality : 0.045 0.180 2804 Planarity : 0.003 0.044 2986 Dihedral : 9.117 73.722 2684 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.99 % Allowed : 23.55 % 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: 0.69 (0.19), residues: 2094 helix: 0.79 (0.23), residues: 540 sheet: 1.15 (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 B 332 HIS 0.003 0.001 HIS B 337 PHE 0.021 0.001 PHE E 221 TYR 0.010 0.001 TYR A 225 ARG 0.009 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 635) hydrogen bonds : angle 5.10768 ( 1728) covalent geometry : bond 0.00300 (17669) covalent geometry : angle 0.48702 (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 225 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 1.913 Fit side-chains revert: symmetry clash REVERT: F 34 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7917 (tptt) REVERT: F 232 PHE cc_start: 0.7687 (m-80) cc_final: 0.7401 (m-80) REVERT: D 21 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.6970 (mt-10) REVERT: D 232 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.7409 (m-80) REVERT: D 245 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7372 (tt) REVERT: E 264 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7262 (mm-30) REVERT: E 330 MET cc_start: 0.7196 (mmm) cc_final: 0.6552 (mmt) REVERT: B 34 LYS cc_start: 0.8239 (ttpt) cc_final: 0.8013 (ttmt) REVERT: B 109 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8256 (mppt) REVERT: B 138 ARG cc_start: 0.8018 (ttp-170) cc_final: 0.7647 (ttt90) REVERT: B 199 ASN cc_start: 0.7272 (m-40) cc_final: 0.7022 (t0) REVERT: B 264 GLU cc_start: 0.6787 (tm-30) cc_final: 0.6497 (tm-30) REVERT: B 345 LEU cc_start: 0.5727 (OUTLIER) cc_final: 0.5475 (pp) REVERT: A 264 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7187 (mt-10) REVERT: A 284 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7048 (tm-30) REVERT: C 188 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8006 (tm-30) outliers start: 35 outliers final: 14 residues processed: 215 average time/residue: 1.1837 time to fit residues: 286.8069 Evaluate side-chains 204 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 109 LYS 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 232 PHE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 188 GLN 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: 2.9990 chunk 114 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 191 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.175402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.137747 restraints weight = 113333.736| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 5.02 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17669 Z= 0.154 Angle : 0.509 8.839 24135 Z= 0.266 Chirality : 0.046 0.189 2804 Planarity : 0.003 0.046 2986 Dihedral : 9.063 71.633 2684 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.94 % Allowed : 23.49 % Favored : 74.57 % 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: 0.61 (0.19), residues: 2094 helix: 0.68 (0.23), residues: 540 sheet: 1.06 (0.29), residues: 342 loop : 0.19 (0.19), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 332 HIS 0.003 0.001 HIS B 337 PHE 0.028 0.002 PHE E 221 TYR 0.011 0.001 TYR C 225 ARG 0.009 0.001 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 635) hydrogen bonds : angle 5.23545 ( 1728) covalent geometry : bond 0.00367 (17669) covalent geometry : angle 0.50874 (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 224 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 1.901 Fit side-chains REVERT: F 34 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7998 (ttpp) REVERT: F 204 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7333 (mmtm) REVERT: F 224 ARG cc_start: 0.7686 (ttm170) cc_final: 0.7465 (ttm-80) REVERT: D 21 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7001 (mt-10) REVERT: D 232 PHE cc_start: 0.7637 (OUTLIER) cc_final: 0.7390 (m-80) REVERT: D 245 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7419 (tt) REVERT: E 264 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7282 (mm-30) REVERT: B 34 LYS cc_start: 0.8282 (ttpt) cc_final: 0.8047 (ttmt) REVERT: B 138 ARG cc_start: 0.7996 (ttp-170) cc_final: 0.7629 (ttt90) REVERT: B 199 ASN cc_start: 0.7326 (m-40) cc_final: 0.7095 (t0) REVERT: B 264 GLU cc_start: 0.6846 (tm-30) cc_final: 0.6587 (tm-30) REVERT: B 345 LEU cc_start: 0.5928 (OUTLIER) cc_final: 0.5657 (pp) REVERT: A 264 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7194 (mt-10) REVERT: A 284 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.6963 (tm-30) outliers start: 34 outliers final: 17 residues processed: 212 average time/residue: 1.2044 time to fit residues: 288.0649 Evaluate side-chains 212 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 204 LYS Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 91 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: 0.6980 chunk 10 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.175201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.137518 restraints weight = 116458.353| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 5.06 r_work: 0.3149 rms_B_bonded: 5.02 restraints_weight: 2.0000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17669 Z= 0.158 Angle : 0.512 8.950 24135 Z= 0.268 Chirality : 0.046 0.195 2804 Planarity : 0.003 0.046 2986 Dihedral : 8.868 67.348 2684 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.67 % Allowed : 24.09 % Favored : 74.25 % 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: 0.56 (0.19), residues: 2094 helix: 0.55 (0.23), residues: 546 sheet: 1.05 (0.29), residues: 342 loop : 0.20 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 332 HIS 0.003 0.001 HIS B 337 PHE 0.030 0.002 PHE E 221 TYR 0.011 0.001 TYR C 225 ARG 0.009 0.001 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 635) hydrogen bonds : angle 5.26133 ( 1728) covalent geometry : bond 0.00379 (17669) covalent geometry : angle 0.51244 (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 220 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 1.852 Fit side-chains REVERT: F 21 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8139 (mt-10) REVERT: F 34 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8434 (ttpp) REVERT: F 204 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7289 (mmtt) REVERT: D 21 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7544 (mt-10) REVERT: D 232 PHE cc_start: 0.7587 (OUTLIER) cc_final: 0.7267 (m-80) REVERT: D 245 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7554 (tt) REVERT: E 264 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7513 (mm-30) REVERT: B 34 LYS cc_start: 0.8786 (ttpt) cc_final: 0.8380 (ttmt) REVERT: B 138 ARG cc_start: 0.8463 (ttp-170) cc_final: 0.7826 (ttt90) REVERT: B 199 ASN cc_start: 0.7969 (m-40) cc_final: 0.7514 (t0) REVERT: B 264 GLU cc_start: 0.6904 (tm-30) cc_final: 0.6620 (tm-30) REVERT: A 220 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7312 (tp30) REVERT: A 264 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7664 (mt-10) REVERT: A 284 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7166 (tm-30) REVERT: A 345 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5628 (tt) REVERT: C 138 ARG cc_start: 0.8277 (mtp85) cc_final: 0.7421 (ttp-170) outliers start: 29 outliers final: 14 residues processed: 211 average time/residue: 1.2198 time to fit residues: 289.5785 Evaluate side-chains 208 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 204 LYS Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 91 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: 0.9980 chunk 148 optimal weight: 0.3980 chunk 134 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 53 optimal weight: 0.1980 chunk 42 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.176788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.139640 restraints weight = 98355.047| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 4.87 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1753 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= 0.117 Angle : 0.488 12.024 24135 Z= 0.255 Chirality : 0.045 0.192 2804 Planarity : 0.003 0.036 2986 Dihedral : 8.660 63.271 2684 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.34 % Allowed : 24.41 % Favored : 74.25 % 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: 0.65 (0.19), residues: 2094 helix: 0.70 (0.23), residues: 540 sheet: 1.07 (0.29), residues: 342 loop : 0.22 (0.19), residues: 1212 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 0.027 0.001 PHE E 221 TYR 0.009 0.001 TYR C 225 ARG 0.007 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.03320 ( 635) hydrogen bonds : angle 5.07059 ( 1728) covalent geometry : bond 0.00272 (17669) covalent geometry : angle 0.48846 (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 212 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 2.037 Fit side-chains REVERT: F 21 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7557 (mt-10) REVERT: F 34 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7812 (tptm) REVERT: D 21 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7003 (mt-10) REVERT: D 232 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.7387 (m-80) REVERT: D 245 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7403 (tt) REVERT: E 264 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7254 (mm-30) REVERT: B 34 LYS cc_start: 0.8233 (ttpt) cc_final: 0.8003 (ttmt) REVERT: B 138 ARG cc_start: 0.8011 (ttp-170) cc_final: 0.7637 (ttt90) REVERT: B 199 ASN cc_start: 0.7330 (m-40) cc_final: 0.7112 (t0) REVERT: B 264 GLU cc_start: 0.6886 (tm-30) cc_final: 0.6615 (tm-30) REVERT: A 220 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7451 (tp30) REVERT: A 264 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7204 (mt-10) REVERT: A 284 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.6961 (tm-30) REVERT: C 208 GLN cc_start: 0.7507 (tp-100) cc_final: 0.7277 (tm-30) outliers start: 22 outliers final: 15 residues processed: 204 average time/residue: 1.2236 time to fit residues: 280.9244 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 : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain C residue 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 6 optimal weight: 0.0670 chunk 44 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 chunk 136 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.176515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.139133 restraints weight = 105963.250| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 4.87 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1765 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= 0.123 Angle : 0.489 11.447 24135 Z= 0.255 Chirality : 0.045 0.191 2804 Planarity : 0.003 0.035 2986 Dihedral : 8.599 58.972 2684 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.56 % Allowed : 24.03 % 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: 0.65 (0.19), residues: 2094 helix: 0.63 (0.23), residues: 546 sheet: 1.22 (0.30), residues: 312 loop : 0.23 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 332 HIS 0.003 0.001 HIS B 337 PHE 0.029 0.001 PHE E 221 TYR 0.012 0.001 TYR F 225 ARG 0.007 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.03362 ( 635) hydrogen bonds : angle 5.08292 ( 1728) covalent geometry : bond 0.00288 (17669) covalent geometry : angle 0.48942 (24135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10751.64 seconds wall clock time: 186 minutes 31.42 seconds (11191.42 seconds total)