Starting phenix.real_space_refine on Thu Aug 6 20:27:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ud3_42145/08_2026/8ud3_42145.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ud3_42145/08_2026/8ud3_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ud3_42145/08_2026/8ud3_42145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ud3_42145/08_2026/8ud3_42145.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ud3_42145/08_2026/8ud3_42145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ud3_42145/08_2026/8ud3_42145.map" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 34 5.49 5 S 60 5.16 5 C 10943 2.51 5 N 2807 2.21 5 O 3400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17244 Number of models: 1 Model: "" Number of chains: 8 Chain: "F" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "D" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "E" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "B" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "A" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "C" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "G" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 340 Classifications: {'RNA': 17} Modifications used: {'rna3p_pyr': 17} Link IDs: {'rna3p': 16} Chain: "H" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 374 Classifications: {'RNA': 17} Modifications used: {'rna3p_pur': 17} Link IDs: {'rna3p': 16} Residues with excluded nonbonded symmetry interactions: 18 residue: pdb=" N AILE F 27 " occ=0.52 ... (14 atoms not shown) pdb=" CD1BILE F 27 " occ=0.48 residue: pdb=" N AASN F 28 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN F 28 " occ=0.48 residue: pdb=" N AASN F 29 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN F 29 " occ=0.48 residue: pdb=" N AILE D 27 " occ=0.52 ... (14 atoms not shown) pdb=" CD1BILE D 27 " occ=0.48 residue: pdb=" N AASN D 28 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN D 28 " occ=0.48 residue: pdb=" N AASN D 29 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN D 29 " occ=0.48 residue: pdb=" N AILE E 27 " occ=0.52 ... (14 atoms not shown) pdb=" CD1BILE E 27 " occ=0.48 residue: pdb=" N AASN E 28 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN E 28 " occ=0.48 residue: pdb=" N AASN E 29 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN E 29 " occ=0.48 residue: pdb=" N AILE B 27 " occ=0.52 ... (14 atoms not shown) pdb=" CD1BILE B 27 " occ=0.48 residue: pdb=" N AASN B 28 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN B 28 " occ=0.48 residue: pdb=" N AASN B 29 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN B 29 " occ=0.48 ... (remaining 6 not shown) Time building chain proxies: 6.47, per 1000 atoms: 0.38 Number of scatterers: 17244 At special positions: 0 Unit cell: (114.08, 122.36, 133.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 34 15.00 O 3400 8.00 N 2807 7.00 C 10943 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 1.3 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: 1.99 Creating SS restraints... Processing helix chain 'F' and resid 1 through 13 Processing helix chain 'F' and resid 50 through 60 Processing helix chain 'F' and resid 68 through 75 Processing helix chain 'F' and resid 113 through 117 Processing helix chain 'F' and resid 129 through 137 Processing helix chain 'F' and resid 207 through 216 Processing helix chain 'F' and resid 217 through 225 Processing helix chain 'F' and resid 231 through 236 Processing helix chain 'F' and resid 250 through 261 removed outlier: 3.567A pdb=" N GLU F 260 " --> pdb=" O LYS F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 308 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 50 through 60 Processing helix chain 'D' and resid 68 through 75 Processing helix chain 'D' and resid 113 through 117 Processing helix chain 'D' and resid 129 through 137 Processing helix chain 'D' and resid 207 through 216 Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 231 through 236 removed outlier: 3.509A pdb=" N VAL D 236 " --> pdb=" O PHE D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.589A pdb=" N GLU D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 50 through 60 Processing helix chain 'E' and resid 68 through 75 Processing helix chain 'E' and resid 113 through 117 Processing helix chain 'E' and resid 129 through 136 Processing helix chain 'E' and resid 207 through 216 Processing helix chain 'E' and resid 217 through 225 Processing helix chain 'E' and resid 231 through 236 Processing helix chain 'E' and resid 250 through 261 removed outlier: 3.526A pdb=" N GLU E 260 " --> pdb=" O LYS E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 308 Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 50 through 60 Processing helix chain 'B' and resid 68 through 75 Processing helix chain 'B' and resid 113 through 117 Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 207 through 216 Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.550A pdb=" N GLU B 260 " --> pdb=" O LYS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 68 through 75 Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.665A pdb=" N GLU A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 308 Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 50 through 60 Processing helix chain 'C' and resid 68 through 75 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 129 through 136 Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.637A pdb=" N GLU C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 308 Processing sheet with id=AA1, first strand: chain 'F' and resid 24 through 27 removed outlier: 6.567A pdb=" N VAL F 31 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 79 through 80 removed outlier: 7.086A pdb=" N ILE F 79 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N ASP F 124 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LYS F 180 " --> pdb=" O GLN F 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'F' and resid 98 through 99 removed outlier: 8.036A pdb=" N THR F 98 " --> pdb=" O ILE F 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AA6, first strand: chain 'F' and resid 264 through 266 removed outlier: 4.958A pdb=" N ILE F 280 " --> pdb=" O CYS F 290 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N CYS F 290 " --> pdb=" O ILE F 280 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 315 through 322 removed outlier: 7.345A pdb=" N SER F 328 " --> pdb=" O PRO F 343 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N MET F 330 " --> pdb=" O PHE F 341 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE F 341 " --> pdb=" O MET F 330 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP F 332 " --> pdb=" O GLU F 339 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 24 through 27 removed outlier: 6.605A pdb=" N VAL D 31 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 79 through 80 removed outlier: 7.194A pdb=" N ILE D 79 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ASP D 124 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 79 through 80 removed outlier: 7.194A pdb=" N ILE D 79 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ASP D 124 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS D 180 " --> pdb=" O GLN D 187 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 86 through 87 Processing sheet with id=AB3, first strand: chain 'D' and resid 98 through 99 removed outlier: 8.016A pdb=" N THR D 98 " --> pdb=" O ILE D 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 160 through 162 Processing sheet with id=AB5, first strand: chain 'D' and resid 264 through 266 removed outlier: 4.949A pdb=" N ILE D 280 " --> pdb=" O CYS D 290 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N CYS D 290 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 315 through 322 removed outlier: 5.863A pdb=" N LYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL D 338 " --> pdb=" O LYS D 334 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 24 through 27 removed outlier: 6.594A pdb=" N VAL E 31 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.098A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N ASP E 124 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.098A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N ASP E 124 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LYS E 180 " --> pdb=" O GLN E 187 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AC2, first strand: chain 'E' and resid 98 through 99 removed outlier: 8.124A pdb=" N THR E 98 " --> pdb=" O ILE E 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 160 through 162 Processing sheet with id=AC4, first strand: chain 'E' and resid 264 through 266 removed outlier: 4.973A pdb=" N ILE E 280 " --> pdb=" O CYS E 290 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N CYS E 290 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 315 through 322 removed outlier: 7.154A pdb=" N SER E 328 " --> pdb=" O PRO E 343 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N MET E 330 " --> pdb=" O PHE E 341 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE E 341 " --> pdb=" O MET E 330 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP E 332 " --> pdb=" O GLU E 339 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 24 through 27 removed outlier: 6.634A pdb=" N VAL B 31 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.133A pdb=" N ILE B 79 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ASP B 124 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.133A pdb=" N ILE B 79 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ASP B 124 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LYS B 180 " --> pdb=" O GLN B 187 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AD1, first strand: chain 'B' and resid 98 through 99 removed outlier: 8.114A pdb=" N THR B 98 " --> pdb=" O ILE B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AD3, first strand: chain 'B' and resid 264 through 266 removed outlier: 4.935A pdb=" N ILE B 280 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N CYS B 290 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 315 through 322 removed outlier: 7.198A pdb=" N SER B 328 " --> pdb=" O PRO B 343 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N MET B 330 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE B 341 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP B 332 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 24 through 26 removed outlier: 6.651A pdb=" N VAL A 31 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.082A pdb=" N ILE A 79 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ASP A 124 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.082A pdb=" N ILE A 79 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ASP A 124 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS A 180 " --> pdb=" O GLN A 187 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AD9, first strand: chain 'A' and resid 98 through 99 removed outlier: 8.093A pdb=" N THR A 98 " --> pdb=" O ILE A 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AE2, first strand: chain 'A' and resid 264 through 266 removed outlier: 5.000A pdb=" N ILE A 280 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N CYS A 290 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 316 through 322 removed outlier: 3.956A pdb=" N TYR A 342 " --> pdb=" O MET A 330 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 24 through 26 removed outlier: 6.599A pdb=" N VAL C 31 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.129A pdb=" N ILE C 79 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N ASP C 124 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.129A pdb=" N ILE C 79 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N ASP C 124 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LYS C 180 " --> pdb=" O GLN C 187 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AE8, first strand: chain 'C' and resid 98 through 99 removed outlier: 8.042A pdb=" N THR C 98 " --> pdb=" O ILE C 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 160 through 162 Processing sheet with id=AF1, first strand: chain 'C' and resid 264 through 266 removed outlier: 4.792A pdb=" N ILE C 280 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N CYS C 290 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 315 through 322 removed outlier: 7.117A pdb=" N SER C 328 " --> pdb=" O PRO C 343 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N MET C 330 " --> pdb=" O PHE C 341 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE C 341 " --> pdb=" O MET C 330 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP C 332 " --> pdb=" O GLU C 339 " (cutoff:3.500A) 650 hydrogen bonds defined for protein. 1668 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 3.45 Time building geometry restraints manager: 1.58 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: 23900 2.08 - 4.15: 212 4.15 - 6.23: 17 6.23 - 8.31: 3 8.31 - 10.39: 3 Bond angle restraints: 24135 Sorted by residual: 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=" 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 1.60e+00 3.91e-01 1.39e+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=" O4' A H 15 " pdb=" C1' A H 15 " pdb=" C2' A H 15 " ideal model delta sigma weight residual 107.60 104.77 2.83 9.00e-01 1.23e+00 9.88e+00 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 ... (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: 2093 0.046 - 0.092: 477 0.092 - 0.138: 207 0.138 - 0.184: 22 0.184 - 0.230: 5 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=" C3' A H 1 " pdb=" C4' A H 1 " pdb=" O3' A H 1 " pdb=" C2' A H 1 " both_signs ideal model delta sigma weight residual False -2.48 -2.67 0.19 2.00e-01 2.50e+01 9.38e-01 ... (remaining 2801 not shown) Planarity restraints: 2986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 204 " 0.050 5.00e-02 4.00e+02 7.57e-02 9.16e+00 pdb=" N PRO F 205 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO F 205 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 205 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 269 " -0.028 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO B 270 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 345 " 0.007 2.00e-02 2.50e+03 1.50e-02 2.24e+00 pdb=" C LEU F 345 " -0.026 2.00e-02 2.50e+03 pdb=" O LEU F 345 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN F 346 " 0.009 2.00e-02 2.50e+03 ... (remaining 2983 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2005 2.75 - 3.29: 16400 3.29 - 3.83: 30887 3.83 - 4.36: 38106 4.36 - 4.90: 63296 Nonbonded interactions: 150694 Sorted by model distance: nonbonded pdb=" OH TYR A 193 " pdb=" OE2 GLU A 304 " model vdw 2.217 3.040 nonbonded pdb=" O HIS D 242 " pdb=" OG SER D 287 " model vdw 2.223 3.040 nonbonded pdb=" O HIS E 242 " pdb=" OG SER E 287 " model vdw 2.245 3.040 nonbonded pdb=" O HIS C 242 " pdb=" OG SER C 287 " model vdw 2.245 3.040 nonbonded pdb=" NH1 ARG E 198 " pdb=" OE1 GLU E 210 " model vdw 2.251 3.120 ... (remaining 150689 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'B' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'C' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'D' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'E' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'F' and (resid 1 through 26 or resid 30 through 346)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.48 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 21.320 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 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= 0.158 Angle : 0.515 10.385 24135 Z= 0.297 Chirality : 0.048 0.230 2804 Planarity : 0.003 0.076 2986 Dihedral : 18.218 105.447 6650 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.65 % Allowed : 23.92 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.19), residues: 2094 helix: 0.52 (0.23), residues: 534 sheet: 0.53 (0.28), residues: 342 loop : 0.27 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 135 TYR 0.008 0.001 TYR F 342 PHE 0.018 0.001 PHE D 258 TRP 0.018 0.001 TRP A 332 HIS 0.013 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.16 (17669) covalent geometry : angle 0.51526 / 0.30 (24135) hydrogen bonds : bond 0.18610 / 12.04 ( 635) hydrogen bonds : angle 8.37318 / 6.01 ( 1728) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 0.740 Fit side-chains REVERT: E 16 ASP cc_start: 0.8143 (t0) cc_final: 0.7497 (t70) REVERT: E 188 GLN cc_start: 0.7816 (tp40) cc_final: 0.7324 (tm-30) REVERT: B 266 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7458 (tt0) REVERT: A 345 LEU cc_start: 0.5690 (OUTLIER) cc_final: 0.5008 (tt) REVERT: C 191 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7769 (mm-30) outliers start: 12 outliers final: 3 residues processed: 201 average time/residue: 0.6212 time to fit residues: 139.7447 Evaluate side-chains 182 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 177 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 328 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 HIS C 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.165155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.111684 restraints weight = 107086.552| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.95 r_work: 0.2864 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17669 Z= 0.227 Angle : 0.577 9.951 24135 Z= 0.308 Chirality : 0.049 0.200 2804 Planarity : 0.004 0.061 2986 Dihedral : 10.588 82.826 2693 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.90 % Allowed : 21.99 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.19), residues: 2094 helix: 0.29 (0.22), residues: 540 sheet: 0.55 (0.28), residues: 354 loop : 0.23 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 126 TYR 0.015 0.002 TYR E 225 PHE 0.017 0.002 PHE B 15 TRP 0.013 0.002 TRP A 332 HIS 0.012 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.23 (17669) covalent geometry : angle 0.57697 / 0.31 (24135) hydrogen bonds : bond 0.05083 / 3.39 ( 635) hydrogen bonds : angle 6.23301 / 4.45 ( 1728) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 187 time to evaluate : 0.669 Fit side-chains REVERT: F 103 SER cc_start: 0.8830 (OUTLIER) cc_final: 0.8496 (p) REVERT: F 187 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7610 (mt0) REVERT: F 224 ARG cc_start: 0.7417 (ttm170) cc_final: 0.6839 (ttm-80) REVERT: F 228 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6735 (mp0) REVERT: D 21 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7595 (mt-10) REVERT: E 21 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.7985 (mt-10) REVERT: E 220 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.6163 (mp0) REVERT: E 264 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7500 (mm-30) REVERT: B 266 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7558 (tt0) REVERT: B 345 LEU cc_start: 0.6025 (OUTLIER) cc_final: 0.5809 (pp) REVERT: A 328 SER cc_start: 0.8836 (p) cc_final: 0.8611 (m) REVERT: A 345 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.5811 (tp) REVERT: C 191 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8083 (mm-30) outliers start: 52 outliers final: 12 residues processed: 221 average time/residue: 0.6469 time to fit residues: 159.4602 Evaluate side-chains 200 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain E residue 21 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 192 THR Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 147 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 80 optimal weight: 1.9990 chunk 138 optimal weight: 0.3980 chunk 135 optimal weight: 8.9990 chunk 204 optimal weight: 20.0000 chunk 6 optimal weight: 0.0470 chunk 73 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 198 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 346 GLN A 337 HIS C 14 HIS C 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.168506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.115280 restraints weight = 104009.526| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 4.04 r_work: 0.2838 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 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 = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17669 Z= 0.118 Angle : 0.491 8.892 24135 Z= 0.263 Chirality : 0.045 0.159 2804 Planarity : 0.003 0.050 2986 Dihedral : 10.117 81.802 2690 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.31 % Allowed : 22.26 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.19), residues: 2094 helix: 0.52 (0.23), residues: 540 sheet: 0.63 (0.28), residues: 324 loop : 0.21 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 138 TYR 0.009 0.001 TYR F 225 PHE 0.013 0.001 PHE E 240 TRP 0.011 0.001 TRP A 332 HIS 0.012 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (17669) covalent geometry : angle 0.49081 / 0.26 (24135) hydrogen bonds : bond 0.04310 / 2.87 ( 635) hydrogen bonds : angle 5.79424 / 4.15 ( 1728) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 0.539 Fit side-chains REVERT: F 21 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8085 (mt-10) REVERT: F 187 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7545 (mt0) REVERT: F 339 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7325 (pt0) REVERT: D 21 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7581 (mt-10) REVERT: D 232 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.7101 (m-80) REVERT: D 254 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6919 (tp) REVERT: E 220 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.6071 (mp0) REVERT: E 241 SER cc_start: 0.8823 (m) cc_final: 0.8619 (m) REVERT: E 264 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7399 (mm-30) REVERT: E 346 GLN cc_start: 0.4610 (OUTLIER) cc_final: 0.4399 (tp-100) REVERT: B 264 GLU cc_start: 0.6845 (tm-30) cc_final: 0.6550 (tm-30) REVERT: B 345 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5846 (pp) REVERT: A 284 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7270 (tm-30) REVERT: A 345 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.5691 (tt) REVERT: C 12 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8069 (mttt) REVERT: C 191 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7893 (mm-30) outliers start: 41 outliers final: 8 residues processed: 219 average time/residue: 0.6008 time to fit residues: 147.4394 Evaluate side-chains 197 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 339 GLU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 346 GLN 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 96 ILE Chi-restraints excluded: chain A residue 214 LEU 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 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 89 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 120 optimal weight: 0.0030 chunk 28 optimal weight: 0.9990 chunk 197 optimal weight: 0.7980 chunk 176 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 163 ASN D 277 ASN E 346 GLN A 337 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.166257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.114123 restraints weight = 102220.006| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.54 r_work: 0.2859 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 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 = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1053 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= 0.136 Angle : 0.496 9.645 24135 Z= 0.265 Chirality : 0.046 0.175 2804 Planarity : 0.003 0.045 2986 Dihedral : 9.812 80.887 2686 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.31 % Allowed : 22.53 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.19), residues: 2094 helix: 0.57 (0.23), residues: 540 sheet: 0.67 (0.28), residues: 324 loop : 0.21 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 138 TYR 0.010 0.001 TYR E 225 PHE 0.012 0.001 PHE C 329 TRP 0.006 0.001 TRP D 332 HIS 0.009 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (17669) covalent geometry : angle 0.49551 / 0.27 (24135) hydrogen bonds : bond 0.04058 / 2.70 ( 635) hydrogen bonds : angle 5.63175 / 4.03 ( 1728) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 180 time to evaluate : 0.670 Fit side-chains REVERT: F 21 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: F 187 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7599 (mt0) REVERT: D 21 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7585 (mt-10) REVERT: D 232 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.7122 (m-80) REVERT: D 245 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7324 (tt) REVERT: D 254 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6934 (tp) REVERT: D 284 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: E 264 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7424 (mm-30) REVERT: B 264 GLU cc_start: 0.6864 (tm-30) cc_final: 0.6570 (tm-30) REVERT: B 344 LYS cc_start: 0.7032 (OUTLIER) cc_final: 0.6784 (tmtt) REVERT: B 345 LEU cc_start: 0.6101 (OUTLIER) cc_final: 0.5750 (pp) REVERT: A 232 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.6917 (t80) REVERT: A 264 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7557 (mt-10) REVERT: A 284 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7258 (tm-30) REVERT: A 345 LEU cc_start: 0.6429 (OUTLIER) cc_final: 0.5694 (tt) REVERT: C 12 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8040 (mttt) REVERT: C 152 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.6940 (pm20) REVERT: C 191 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7877 (mm-30) outliers start: 41 outliers final: 13 residues processed: 210 average time/residue: 0.5986 time to fit residues: 141.4349 Evaluate side-chains 201 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 91 ASP 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 254 LEU Chi-restraints excluded: chain D residue 284 GLN Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 261 SER 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 147 SER Chi-restraints excluded: chain C residue 152 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 346 GLN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.164555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.110826 restraints weight = 101435.625| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.82 r_work: 0.2768 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 17669 Z= 0.299 Angle : 0.608 9.672 24135 Z= 0.323 Chirality : 0.052 0.214 2804 Planarity : 0.004 0.043 2986 Dihedral : 9.862 80.402 2686 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.12 % Allowed : 22.37 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.18), residues: 2094 helix: 0.24 (0.22), residues: 534 sheet: 0.76 (0.28), residues: 342 loop : 0.01 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 90 TYR 0.017 0.002 TYR E 225 PHE 0.020 0.002 PHE C 329 TRP 0.008 0.002 TRP B 332 HIS 0.005 0.001 HIS F 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00724 / 0.30 (17669) covalent geometry : angle 0.60773 / 0.32 (24135) hydrogen bonds : bond 0.04967 / 3.32 ( 635) hydrogen bonds : angle 5.97375 / 4.24 ( 1728) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 182 time to evaluate : 1.173 Fit side-chains REVERT: F 21 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8175 (mt-10) REVERT: F 34 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8499 (ttpp) REVERT: F 187 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7606 (mt0) REVERT: F 204 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.7218 (mmtm) REVERT: F 224 ARG cc_start: 0.7393 (ttm170) cc_final: 0.6818 (ttm-80) REVERT: D 21 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7569 (mt-10) REVERT: D 232 PHE cc_start: 0.7477 (OUTLIER) cc_final: 0.7196 (m-80) REVERT: D 254 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.7006 (tp) REVERT: E 264 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7455 (mm-30) REVERT: B 218 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.7265 (ttm) REVERT: B 264 GLU cc_start: 0.6882 (tm-30) cc_final: 0.6599 (tm-30) REVERT: B 344 LYS cc_start: 0.7084 (OUTLIER) cc_final: 0.6791 (tmtt) REVERT: B 345 LEU cc_start: 0.5944 (OUTLIER) cc_final: 0.5597 (pp) REVERT: A 264 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7589 (mt-10) REVERT: A 284 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7193 (tm-30) REVERT: A 345 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.5928 (tt) REVERT: C 12 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8123 (mttt) REVERT: C 152 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.6958 (pm20) REVERT: C 191 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7960 (mm-30) outliers start: 54 outliers final: 20 residues processed: 219 average time/residue: 0.6263 time to fit residues: 153.6416 Evaluate side-chains 209 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 187 GLN 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 170 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 152 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 60 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 27 optimal weight: 0.0970 chunk 95 optimal weight: 0.5980 chunk 168 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 119 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.175100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.137619 restraints weight = 113510.480| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 4.99 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1286 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= 0.125 Angle : 0.495 9.401 24135 Z= 0.264 Chirality : 0.046 0.170 2804 Planarity : 0.003 0.038 2986 Dihedral : 9.575 79.366 2686 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.37 % Allowed : 23.01 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.19), residues: 2094 helix: 0.51 (0.23), residues: 534 sheet: 0.65 (0.29), residues: 354 loop : 0.05 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 138 TYR 0.009 0.001 TYR C 225 PHE 0.011 0.001 PHE D 329 TRP 0.006 0.001 TRP B 332 HIS 0.003 0.001 HIS B 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (17669) covalent geometry : angle 0.49503 / 0.26 (24135) hydrogen bonds : bond 0.03921 / 2.62 ( 635) hydrogen bonds : angle 5.51585 / 3.96 ( 1728) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.615 Fit side-chains REVERT: F 21 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: F 187 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.7106 (mt0) REVERT: F 204 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7516 (mmtt) REVERT: F 232 PHE cc_start: 0.7730 (m-80) cc_final: 0.7356 (m-80) REVERT: D 21 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.6918 (mt-10) REVERT: D 232 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7387 (m-80) REVERT: D 330 MET cc_start: 0.7143 (mmp) cc_final: 0.6374 (mpp) REVERT: D 344 LYS cc_start: 0.6852 (OUTLIER) cc_final: 0.6544 (ptmm) REVERT: E 264 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7317 (mm-30) REVERT: B 264 GLU cc_start: 0.6809 (tm-30) cc_final: 0.6593 (tm-30) REVERT: B 344 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.7064 (tmtt) REVERT: B 345 LEU cc_start: 0.6059 (OUTLIER) cc_final: 0.5727 (pp) REVERT: A 264 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7252 (mt-10) REVERT: A 284 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.6996 (tm-30) REVERT: A 345 LEU cc_start: 0.6076 (OUTLIER) cc_final: 0.5417 (tt) REVERT: A 346 GLN cc_start: 0.5728 (OUTLIER) cc_final: 0.4940 (tm-30) REVERT: C 12 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7821 (mttt) outliers start: 39 outliers final: 15 residues processed: 212 average time/residue: 0.5836 time to fit residues: 138.7424 Evaluate side-chains 197 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 187 GLN 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 344 LYS Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 152 GLN 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 A residue 345 LEU Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 147 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 172 optimal weight: 0.2980 chunk 39 optimal weight: 0.3980 chunk 154 optimal weight: 0.4980 chunk 44 optimal weight: 0.0050 chunk 65 optimal weight: 3.9990 chunk 120 optimal weight: 0.4980 chunk 188 optimal weight: 0.4980 chunk 189 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.177105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.140437 restraints weight = 106658.422| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 4.88 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17669 Z= 0.101 Angle : 0.469 9.282 24135 Z= 0.251 Chirality : 0.045 0.167 2804 Planarity : 0.003 0.036 2986 Dihedral : 9.341 77.041 2686 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.26 % Allowed : 23.23 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.19), residues: 2094 helix: 0.63 (0.23), residues: 540 sheet: 0.75 (0.29), residues: 324 loop : 0.13 (0.19), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 138 TYR 0.010 0.001 TYR F 225 PHE 0.010 0.001 PHE A 268 TRP 0.007 0.001 TRP D 332 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (17669) covalent geometry : angle 0.46938 / 0.25 (24135) hydrogen bonds : bond 0.03566 / 2.36 ( 635) hydrogen bonds : angle 5.19270 / 3.73 ( 1728) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 0.421 Fit side-chains REVERT: F 21 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7604 (mt-10) REVERT: F 103 SER cc_start: 0.8513 (OUTLIER) cc_final: 0.8197 (p) REVERT: F 345 LEU cc_start: 0.4189 (OUTLIER) cc_final: 0.3331 (mt) REVERT: D 232 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7367 (m-80) REVERT: D 245 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7378 (tt) REVERT: D 330 MET cc_start: 0.7132 (mmp) cc_final: 0.6354 (mpp) REVERT: E 264 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7246 (mm-30) REVERT: B 264 GLU cc_start: 0.6759 (tm-30) cc_final: 0.6500 (tm-30) REVERT: B 344 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.7015 (tmtt) REVERT: B 345 LEU cc_start: 0.6069 (OUTLIER) cc_final: 0.5758 (pp) REVERT: A 264 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7214 (mt-10) REVERT: A 284 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7008 (tm-30) REVERT: A 345 LEU cc_start: 0.5924 (OUTLIER) cc_final: 0.5244 (tt) REVERT: A 346 GLN cc_start: 0.5359 (OUTLIER) cc_final: 0.4664 (tm-30) REVERT: C 306 ILE cc_start: 0.7167 (tt) cc_final: 0.6690 (pt) outliers start: 37 outliers final: 9 residues processed: 216 average time/residue: 0.5498 time to fit residues: 134.5352 Evaluate side-chains 197 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 346 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 170 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 60 optimal weight: 0.0870 chunk 180 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 136 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.176003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.138831 restraints weight = 103809.081| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 4.79 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3593 r_free = 0.3593 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3593 r_free = 0.3593 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1445 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= 0.127 Angle : 0.483 9.024 24135 Z= 0.257 Chirality : 0.045 0.175 2804 Planarity : 0.003 0.047 2986 Dihedral : 9.336 76.117 2686 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.88 % Allowed : 24.14 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.19), residues: 2094 helix: 0.65 (0.23), residues: 540 sheet: 0.71 (0.28), residues: 354 loop : 0.15 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 138 TYR 0.010 0.001 TYR C 225 PHE 0.034 0.001 PHE E 221 TRP 0.006 0.001 TRP B 332 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (17669) covalent geometry : angle 0.48277 / 0.26 (24135) hydrogen bonds : bond 0.03720 / 2.48 ( 635) hydrogen bonds : angle 5.22387 / 3.75 ( 1728) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.569 Fit side-chains REVERT: F 21 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7595 (mt-10) REVERT: F 103 SER cc_start: 0.8574 (OUTLIER) cc_final: 0.8248 (p) REVERT: F 224 ARG cc_start: 0.7754 (ttm170) cc_final: 0.7198 (ttm-80) REVERT: F 345 LEU cc_start: 0.4251 (OUTLIER) cc_final: 0.3324 (mp) REVERT: D 21 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.6887 (mt-10) REVERT: D 44 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: D 232 PHE cc_start: 0.7663 (OUTLIER) cc_final: 0.7377 (m-80) REVERT: D 245 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7406 (tt) REVERT: D 330 MET cc_start: 0.7120 (mmp) cc_final: 0.6303 (mpp) REVERT: D 344 LYS cc_start: 0.7012 (OUTLIER) cc_final: 0.6666 (ptmm) REVERT: E 264 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7227 (mm-30) REVERT: B 34 LYS cc_start: 0.8288 (ttpt) cc_final: 0.8033 (ttmt) REVERT: B 199 ASN cc_start: 0.7200 (m-40) cc_final: 0.6887 (t0) REVERT: B 264 GLU cc_start: 0.6749 (tm-30) cc_final: 0.6509 (tm-30) REVERT: B 344 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.7012 (tmtt) REVERT: B 345 LEU cc_start: 0.6022 (OUTLIER) cc_final: 0.5690 (pp) REVERT: A 264 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7274 (mt-10) REVERT: A 284 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7027 (tm-30) REVERT: A 346 GLN cc_start: 0.5291 (OUTLIER) cc_final: 0.4568 (mp10) REVERT: C 12 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7812 (mtpt) outliers start: 30 outliers final: 12 residues processed: 200 average time/residue: 0.5442 time to fit residues: 123.7067 Evaluate side-chains 201 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 344 LYS Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 214 LEU 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 A residue 346 GLN Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 78 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 33 optimal weight: 5.9990 chunk 155 optimal weight: 0.2980 chunk 71 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 21 optimal weight: 0.3980 chunk 201 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 136 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.175823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.138705 restraints weight = 105234.737| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 4.83 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3591 r_free = 0.3591 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3591 r_free = 0.3591 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1475 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 : 0.483 8.795 24135 Z= 0.257 Chirality : 0.045 0.186 2804 Planarity : 0.003 0.046 2986 Dihedral : 9.270 75.103 2684 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.94 % Allowed : 24.09 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.19), residues: 2094 helix: 0.66 (0.23), residues: 540 sheet: 0.77 (0.29), residues: 354 loop : 0.14 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 138 TYR 0.010 0.001 TYR F 225 PHE 0.031 0.001 PHE E 221 TRP 0.006 0.001 TRP B 332 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (17669) covalent geometry : angle 0.48287 / 0.26 (24135) hydrogen bonds : bond 0.03718 / 2.48 ( 635) hydrogen bonds : angle 5.22225 / 3.75 ( 1728) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.622 Fit side-chains REVERT: F 21 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: F 103 SER cc_start: 0.8562 (OUTLIER) cc_final: 0.8245 (p) REVERT: F 224 ARG cc_start: 0.7721 (ttm170) cc_final: 0.7171 (ttm-80) REVERT: F 232 PHE cc_start: 0.7699 (m-80) cc_final: 0.7327 (m-80) REVERT: F 345 LEU cc_start: 0.4325 (OUTLIER) cc_final: 0.3433 (mt) REVERT: D 232 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.7351 (m-80) REVERT: D 245 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7401 (tt) REVERT: D 284 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7657 (tt0) REVERT: D 330 MET cc_start: 0.7056 (mmp) cc_final: 0.6234 (mpp) REVERT: D 344 LYS cc_start: 0.7030 (OUTLIER) cc_final: 0.6696 (ptmm) REVERT: E 264 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7274 (mm-30) REVERT: B 34 LYS cc_start: 0.8304 (ttpt) cc_final: 0.8040 (ttmt) REVERT: B 138 ARG cc_start: 0.8035 (ttp-170) cc_final: 0.7665 (ttt90) REVERT: B 199 ASN cc_start: 0.7352 (m-40) cc_final: 0.7086 (t0) REVERT: B 264 GLU cc_start: 0.6726 (tm-30) cc_final: 0.6407 (tm-30) REVERT: B 266 GLU cc_start: 0.7523 (tt0) cc_final: 0.7141 (tt0) REVERT: B 344 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.7011 (tmtt) REVERT: B 345 LEU cc_start: 0.5975 (OUTLIER) cc_final: 0.5663 (pp) REVERT: A 264 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7274 (mt-10) REVERT: A 284 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7054 (tm-30) REVERT: A 345 LEU cc_start: 0.5887 (OUTLIER) cc_final: 0.5259 (tt) outliers start: 31 outliers final: 14 residues processed: 198 average time/residue: 0.5611 time to fit residues: 124.9613 Evaluate side-chains 201 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 284 GLN Chi-restraints excluded: chain D residue 344 LYS Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 214 LEU 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 A residue 345 LEU Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 250 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 179 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 166 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 173 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 136 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.175059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.137404 restraints weight = 119051.995| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 5.04 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17669 Z= 0.154 Angle : 0.497 8.815 24135 Z= 0.264 Chirality : 0.046 0.192 2804 Planarity : 0.003 0.048 2986 Dihedral : 9.279 74.585 2684 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.77 % Allowed : 24.30 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.19), residues: 2094 helix: 0.61 (0.23), residues: 540 sheet: 0.77 (0.29), residues: 354 loop : 0.12 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 138 TYR 0.011 0.001 TYR C 225 PHE 0.033 0.002 PHE E 221 TRP 0.006 0.001 TRP B 332 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 (17669) covalent geometry : angle 0.49674 / 0.26 (24135) hydrogen bonds : bond 0.03878 / 2.58 ( 635) hydrogen bonds : angle 5.29012 / 3.79 ( 1728) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 0.789 Fit side-chains REVERT: F 21 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7668 (mt-10) REVERT: F 224 ARG cc_start: 0.7741 (ttm170) cc_final: 0.7171 (ttm-80) REVERT: F 232 PHE cc_start: 0.7637 (m-80) cc_final: 0.7329 (m-80) REVERT: F 345 LEU cc_start: 0.4232 (OUTLIER) cc_final: 0.3357 (mt) REVERT: D 232 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.7354 (m-80) REVERT: D 245 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7440 (tt) REVERT: D 284 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: D 330 MET cc_start: 0.7069 (mmp) cc_final: 0.6258 (mpp) REVERT: D 344 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6716 (ptmm) REVERT: E 264 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7297 (mm-30) REVERT: B 56 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: B 138 ARG cc_start: 0.8027 (ttp-170) cc_final: 0.7669 (ttt90) REVERT: B 199 ASN cc_start: 0.7365 (m-40) cc_final: 0.7117 (t0) REVERT: B 264 GLU cc_start: 0.6832 (tm-30) cc_final: 0.6585 (tm-30) REVERT: B 344 LYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6992 (tmtt) REVERT: B 345 LEU cc_start: 0.5934 (OUTLIER) cc_final: 0.5598 (pp) REVERT: A 264 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7291 (mt-10) REVERT: A 284 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7079 (tm-30) REVERT: A 345 LEU cc_start: 0.5852 (OUTLIER) cc_final: 0.5232 (tt) outliers start: 28 outliers final: 15 residues processed: 197 average time/residue: 0.5270 time to fit residues: 117.2961 Evaluate side-chains 204 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 284 GLN Chi-restraints excluded: chain D residue 344 LYS Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 214 LEU 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 A residue 345 LEU Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 250 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 7 optimal weight: 0.0020 chunk 23 optimal weight: 0.9980 chunk 194 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 0.0980 chunk 165 optimal weight: 0.5980 chunk 196 optimal weight: 0.0170 chunk 72 optimal weight: 0.5980 overall best weight: 0.2626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 136 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.177877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.141535 restraints weight = 109188.884| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 4.86 r_work: 0.3191 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1575 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= 0.091 Angle : 0.463 8.975 24135 Z= 0.246 Chirality : 0.044 0.181 2804 Planarity : 0.003 0.042 2986 Dihedral : 9.144 73.489 2684 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.51 % Allowed : 24.46 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.19), residues: 2094 helix: 0.74 (0.23), residues: 540 sheet: 0.82 (0.30), residues: 324 loop : 0.18 (0.19), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 138 TYR 0.010 0.001 TYR C 225 PHE 0.029 0.001 PHE E 221 TRP 0.006 0.001 TRP D 332 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (17669) covalent geometry : angle 0.46309 / 0.25 (24135) hydrogen bonds : bond 0.03349 / 2.23 ( 635) hydrogen bonds : angle 5.02522 / 3.61 ( 1728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5341.02 seconds wall clock time: 92 minutes 18.86 seconds (5538.86 seconds total)