Starting phenix.real_space_refine on Mon Jul 22 06:06:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud3_42145/07_2024/8ud3_42145.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud3_42145/07_2024/8ud3_42145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud3_42145/07_2024/8ud3_42145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud3_42145/07_2024/8ud3_42145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud3_42145/07_2024/8ud3_42145.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud3_42145/07_2024/8ud3_42145.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 34 5.49 5 S 60 5.16 5 C 10943 2.51 5 N 2807 2.21 5 O 3400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 44": "OE1" <-> "OE2" Residue "F GLU 68": "OE1" <-> "OE2" Residue "F GLU 191": "OE1" <-> "OE2" Residue "F GLU 202": "OE1" <-> "OE2" Residue "F GLU 220": "OE1" <-> "OE2" Residue "F GLU 228": "OE1" <-> "OE2" Residue "F GLU 260": "OE1" <-> "OE2" Residue "D GLU 21": "OE1" <-> "OE2" Residue "D GLU 41": "OE1" <-> "OE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D GLU 264": "OE1" <-> "OE2" Residue "D GLU 266": "OE1" <-> "OE2" Residue "D GLU 326": "OE1" <-> "OE2" Residue "E GLU 21": "OE1" <-> "OE2" Residue "E GLU 41": "OE1" <-> "OE2" Residue "E GLU 44": "OE1" <-> "OE2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E GLU 191": "OE1" <-> "OE2" Residue "E GLU 210": "OE1" <-> "OE2" Residue "E GLU 223": "OE1" <-> "OE2" Residue "E GLU 260": "OE1" <-> "OE2" Residue "E GLU 266": "OE1" <-> "OE2" Residue "B GLU 21": "OE1" <-> "OE2" Residue "B GLU 41": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B GLU 339": "OE1" <-> "OE2" Residue "A GLU 56": "OE1" <-> "OE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 17244 Number of models: 1 Model: "" Number of chains: 8 Chain: "F" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "D" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "E" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "B" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "A" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "C" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "G" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 340 Classifications: {'RNA': 17} Modifications used: {'rna3p_pyr': 17} Link IDs: {'rna3p': 16} Chain: "H" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 374 Classifications: {'RNA': 17} Modifications used: {'rna3p_pur': 17} Link IDs: {'rna3p': 16} Residues with excluded nonbonded symmetry interactions: 18 residue: pdb=" N AILE F 27 " occ=0.52 ... (14 atoms not shown) pdb=" CD1BILE F 27 " occ=0.48 residue: pdb=" N AASN F 28 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN F 28 " occ=0.48 residue: pdb=" N AASN F 29 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN F 29 " occ=0.48 residue: pdb=" N AILE D 27 " occ=0.52 ... (14 atoms not shown) pdb=" CD1BILE D 27 " occ=0.48 residue: pdb=" N AASN D 28 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN D 28 " occ=0.48 residue: pdb=" N AASN D 29 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN D 29 " occ=0.48 residue: pdb=" N AILE E 27 " occ=0.52 ... (14 atoms not shown) pdb=" CD1BILE E 27 " occ=0.48 residue: pdb=" N AASN E 28 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN E 28 " occ=0.48 residue: pdb=" N AASN E 29 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN E 29 " occ=0.48 residue: pdb=" N AILE B 27 " occ=0.52 ... (14 atoms not shown) pdb=" CD1BILE B 27 " occ=0.48 residue: pdb=" N AASN B 28 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN B 28 " occ=0.48 residue: pdb=" N AASN B 29 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN B 29 " occ=0.48 ... (remaining 6 not shown) Time building chain proxies: 17.51, per 1000 atoms: 1.02 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 - 3.50 Amino acid : False - 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: 6.59 Conformation dependent library (CDL) restraints added in 5.8 seconds 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3924 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 47 sheets defined 26.8% alpha, 24.6% beta 15 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 6.36 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: 6.15 Time building geometry restraints manager: 7.26 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: 100.11 - 106.89: 612 106.89 - 113.68: 9925 113.68 - 120.46: 6426 120.46 - 127.24: 6942 127.24 - 134.02: 230 Bond angle restraints: 24135 Sorted by residual: angle pdb=" O3' U G 7 " pdb=" C3' U G 7 " pdb=" C2' U G 7 " ideal model delta sigma weight residual 113.70 107.74 5.96 1.50e+00 4.44e-01 1.58e+01 angle pdb=" C SER C 261 " pdb=" CA SER C 261 " pdb=" CB SER C 261 " ideal model delta sigma weight residual 110.98 106.39 4.59 1.18e+00 7.18e-01 1.52e+01 angle pdb=" N PRO C 262 " pdb=" CA PRO C 262 " pdb=" C PRO C 262 " ideal model delta sigma weight residual 111.14 116.25 -5.11 1.56e+00 4.11e-01 1.07e+01 angle pdb=" CA LEU D 345 " pdb=" CB LEU D 345 " pdb=" CG LEU D 345 " ideal model delta sigma weight residual 116.30 126.69 -10.39 3.50e+00 8.16e-02 8.80e+00 angle pdb=" O3' U G 15 " pdb=" C3' U G 15 " pdb=" C2' U G 15 " ideal model delta sigma weight residual 113.70 109.27 4.43 1.50e+00 4.44e-01 8.71e+00 ... (remaining 24130 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.09: 9382 21.09 - 42.18: 875 42.18 - 63.27: 259 63.27 - 84.36: 38 84.36 - 105.45: 20 Dihedral angle restraints: 10574 sinusoidal: 4490 harmonic: 6084 Sorted by residual: dihedral pdb=" CA THR A 192 " pdb=" C THR A 192 " pdb=" N TYR A 193 " pdb=" CA TYR A 193 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA THR D 192 " pdb=" C THR D 192 " pdb=" N TYR D 193 " pdb=" CA TYR D 193 " ideal model delta harmonic sigma weight residual 180.00 160.53 19.47 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA THR E 192 " pdb=" C THR E 192 " pdb=" N TYR E 193 " pdb=" CA TYR E 193 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 10571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2068 0.046 - 0.092: 471 0.092 - 0.138: 217 0.138 - 0.184: 39 0.184 - 0.230: 9 Chirality restraints: 2804 Sorted by residual: chirality pdb=" C3' U G 15 " pdb=" C4' U G 15 " pdb=" O3' U G 15 " pdb=" C2' U G 15 " both_signs ideal model delta sigma weight residual False -2.48 -2.71 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C3' U G 7 " pdb=" C4' U G 7 " pdb=" O3' U G 7 " pdb=" C2' U G 7 " both_signs ideal model delta sigma weight residual False -2.48 -2.70 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C2' A H 1 " pdb=" C3' A H 1 " pdb=" O2' A H 1 " pdb=" C1' A H 1 " both_signs ideal model delta sigma weight residual False -2.75 -2.56 -0.19 2.00e-01 2.50e+01 9.43e-01 ... (remaining 2801 not shown) Planarity restraints: 2986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 204 " 0.050 5.00e-02 4.00e+02 7.57e-02 9.16e+00 pdb=" N PRO F 205 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO F 205 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 205 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 269 " -0.028 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO B 270 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 345 " 0.007 2.00e-02 2.50e+03 1.50e-02 2.24e+00 pdb=" C LEU F 345 " -0.026 2.00e-02 2.50e+03 pdb=" O LEU F 345 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN F 346 " 0.009 2.00e-02 2.50e+03 ... (remaining 2983 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2005 2.75 - 3.29: 16400 3.29 - 3.83: 30887 3.83 - 4.36: 38106 4.36 - 4.90: 63296 Nonbonded interactions: 150694 Sorted by model distance: nonbonded pdb=" OH TYR A 193 " pdb=" OE2 GLU A 304 " model vdw 2.217 2.440 nonbonded pdb=" O HIS D 242 " pdb=" OG SER D 287 " model vdw 2.223 2.440 nonbonded pdb=" O HIS E 242 " pdb=" OG SER E 287 " model vdw 2.245 2.440 nonbonded pdb=" O HIS C 242 " pdb=" OG SER C 287 " model vdw 2.245 2.440 nonbonded pdb=" NH1 ARG E 198 " pdb=" OE1 GLU E 210 " model vdw 2.251 2.520 ... (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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'B' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'C' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'D' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'E' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'F' and (resid 1 through 26 or resid 30 through 346)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.48 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 62.850 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17669 Z= 0.182 Angle : 0.529 10.385 24135 Z= 0.304 Chirality : 0.050 0.230 2804 Planarity : 0.003 0.076 2986 Dihedral : 18.218 105.447 6650 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.65 % Allowed : 23.92 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.19), residues: 2094 helix: 0.52 (0.23), residues: 534 sheet: 0.53 (0.28), residues: 342 loop : 0.27 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 332 HIS 0.013 0.001 HIS A 337 PHE 0.018 0.001 PHE D 258 TYR 0.008 0.001 TYR F 342 ARG 0.005 0.000 ARG E 135 *********************** 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 fitting. rotamer outliers: 12 poor density : 190 time to evaluate : 1.866 Fit side-chains REVERT: E 16 ASP cc_start: 0.8143 (t0) cc_final: 0.7497 (t70) REVERT: E 188 GLN cc_start: 0.7816 (tp40) cc_final: 0.7324 (tm-30) REVERT: B 266 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7458 (tt0) REVERT: A 345 LEU cc_start: 0.5690 (OUTLIER) cc_final: 0.5007 (tt) REVERT: C 191 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7769 (mm-30) outliers start: 12 outliers final: 3 residues processed: 201 average time/residue: 1.2441 time to fit residues: 280.2921 Evaluate side-chains 181 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 176 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 328 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 0.2980 chunk 156 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 161 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 120 optimal weight: 0.2980 chunk 187 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 346 GLN A 337 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17669 Z= 0.175 Angle : 0.503 8.977 24135 Z= 0.263 Chirality : 0.045 0.175 2804 Planarity : 0.003 0.060 2986 Dihedral : 10.145 82.845 2693 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.42 % Allowed : 22.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.19), residues: 2094 helix: 0.68 (0.23), residues: 546 sheet: 0.93 (0.29), residues: 312 loop : 0.40 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 332 HIS 0.011 0.001 HIS A 337 PHE 0.011 0.001 PHE C 329 TYR 0.010 0.001 TYR F 225 ARG 0.004 0.000 ARG E 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 195 time to evaluate : 1.929 Fit side-chains REVERT: F 187 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7358 (mt0) REVERT: F 228 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6735 (mp0) REVERT: E 16 ASP cc_start: 0.8182 (t0) cc_final: 0.7904 (t70) REVERT: E 220 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.6115 (mp0) REVERT: E 264 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6852 (mm-30) REVERT: E 346 GLN cc_start: 0.4311 (OUTLIER) cc_final: 0.4094 (tp40) REVERT: B 138 ARG cc_start: 0.8281 (ttp-170) cc_final: 0.7831 (ttt90) REVERT: B 264 GLU cc_start: 0.6905 (tm-30) cc_final: 0.6592 (tm-30) REVERT: B 345 LEU cc_start: 0.6112 (OUTLIER) cc_final: 0.5875 (pp) REVERT: A 345 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5304 (tt) REVERT: C 191 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7591 (mm-30) outliers start: 45 outliers final: 9 residues processed: 228 average time/residue: 1.1229 time to fit residues: 290.1545 Evaluate side-chains 198 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 183 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain D residue 300 ASP 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 114 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 187 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 185 optimal weight: 0.3980 chunk 63 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 136 ASN D 277 ASN A 337 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17669 Z= 0.225 Angle : 0.518 11.613 24135 Z= 0.269 Chirality : 0.046 0.183 2804 Planarity : 0.003 0.052 2986 Dihedral : 9.606 81.472 2687 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.53 % Allowed : 22.47 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.19), residues: 2094 helix: 0.60 (0.23), residues: 546 sheet: 0.81 (0.28), residues: 324 loop : 0.32 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 332 HIS 0.010 0.001 HIS A 337 PHE 0.011 0.002 PHE E 268 TYR 0.011 0.001 TYR A 225 ARG 0.006 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 194 time to evaluate : 2.085 Fit side-chains REVERT: F 228 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6825 (mp0) REVERT: D 21 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7340 (mt-10) REVERT: D 232 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.7368 (m-80) REVERT: D 245 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7594 (tt) REVERT: E 16 ASP cc_start: 0.8243 (t0) cc_final: 0.7973 (t70) REVERT: E 21 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7674 (mt-10) REVERT: E 264 GLU cc_start: 0.7260 (mm-30) cc_final: 0.6709 (mm-30) REVERT: B 138 ARG cc_start: 0.8291 (ttp-170) cc_final: 0.7805 (ttt90) REVERT: B 264 GLU cc_start: 0.6858 (tm-30) cc_final: 0.6573 (tm-30) REVERT: B 345 LEU cc_start: 0.6115 (OUTLIER) cc_final: 0.5814 (pp) REVERT: A 264 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7178 (mt-10) REVERT: A 319 LYS cc_start: 0.8151 (mmtp) cc_final: 0.7927 (mptp) REVERT: A 345 LEU cc_start: 0.6014 (OUTLIER) cc_final: 0.5301 (tt) REVERT: A 346 GLN cc_start: 0.5363 (OUTLIER) cc_final: 0.4317 (tm-30) REVERT: C 12 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8005 (mttt) REVERT: C 191 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7571 (mm-30) REVERT: C 242 HIS cc_start: 0.7336 (m-70) cc_final: 0.6995 (m-70) outliers start: 45 outliers final: 19 residues processed: 227 average time/residue: 1.1563 time to fit residues: 296.5939 Evaluate side-chains 208 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 180 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 287 SER 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 Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 345 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 0.2980 chunk 140 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 89 optimal weight: 0.0370 chunk 125 optimal weight: 2.9990 chunk 188 optimal weight: 0.6980 chunk 199 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 136 ASN A 337 HIS C 14 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1203 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= 0.220 Angle : 0.501 9.113 24135 Z= 0.261 Chirality : 0.046 0.190 2804 Planarity : 0.003 0.046 2986 Dihedral : 9.421 78.993 2687 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.69 % Allowed : 22.63 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.19), residues: 2094 helix: 0.62 (0.23), residues: 546 sheet: 0.87 (0.29), residues: 324 loop : 0.31 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 332 HIS 0.010 0.001 HIS A 337 PHE 0.015 0.002 PHE E 258 TYR 0.011 0.001 TYR F 225 ARG 0.005 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 200 time to evaluate : 1.810 Fit side-chains REVERT: F 21 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7935 (mt-10) REVERT: F 232 PHE cc_start: 0.7640 (m-80) cc_final: 0.7260 (m-80) REVERT: F 296 ASP cc_start: 0.8523 (t0) cc_final: 0.8250 (t0) REVERT: D 21 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7336 (mt-10) REVERT: D 232 PHE cc_start: 0.7601 (OUTLIER) cc_final: 0.7330 (m-80) REVERT: D 245 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7595 (tt) REVERT: E 16 ASP cc_start: 0.8249 (t0) cc_final: 0.7985 (t70) REVERT: E 21 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7670 (mt-10) REVERT: E 188 GLN cc_start: 0.7833 (tp40) cc_final: 0.7316 (tm-30) REVERT: E 264 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6774 (mm-30) REVERT: B 138 ARG cc_start: 0.8295 (ttp-170) cc_final: 0.7764 (ttt90) REVERT: B 264 GLU cc_start: 0.6861 (tm-30) cc_final: 0.6608 (tm-30) REVERT: B 345 LEU cc_start: 0.5833 (OUTLIER) cc_final: 0.5602 (pp) REVERT: A 264 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7186 (mt-10) REVERT: A 345 LEU cc_start: 0.5873 (OUTLIER) cc_final: 0.5227 (tt) REVERT: C 12 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8031 (mttt) REVERT: C 110 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8587 (mtmt) REVERT: C 242 HIS cc_start: 0.7476 (m-70) cc_final: 0.7108 (m-70) outliers start: 48 outliers final: 18 residues processed: 236 average time/residue: 1.1775 time to fit residues: 315.5590 Evaluate side-chains 216 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 189 time to evaluate : 1.866 ------------------------------------------------------------------------------- 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 261 SER Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 241 SER 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 243 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 300 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 0.7980 chunk 113 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 148 optimal weight: 0.0570 chunk 82 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1308 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= 0.174 Angle : 0.480 9.438 24135 Z= 0.250 Chirality : 0.045 0.180 2804 Planarity : 0.003 0.041 2986 Dihedral : 9.268 77.204 2687 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.63 % Allowed : 23.01 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.19), residues: 2094 helix: 0.73 (0.23), residues: 546 sheet: 0.93 (0.29), residues: 324 loop : 0.34 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 332 HIS 0.004 0.001 HIS B 337 PHE 0.015 0.001 PHE E 258 TYR 0.010 0.001 TYR E 225 ARG 0.005 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 205 time to evaluate : 1.732 Fit side-chains REVERT: F 103 SER cc_start: 0.8555 (OUTLIER) cc_final: 0.8185 (p) REVERT: F 204 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7163 (mmtm) REVERT: F 232 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.7286 (m-80) REVERT: D 187 GLN cc_start: 0.7305 (mm-40) cc_final: 0.7067 (mm-40) REVERT: D 232 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.7390 (m-80) REVERT: D 245 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7548 (tt) REVERT: D 330 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6037 (mpp) REVERT: E 16 ASP cc_start: 0.8248 (t0) cc_final: 0.7984 (t70) REVERT: E 21 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7678 (mt-10) REVERT: E 188 GLN cc_start: 0.7829 (tp40) cc_final: 0.7312 (tm-30) REVERT: E 264 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6662 (mm-30) REVERT: B 34 LYS cc_start: 0.8432 (ttpt) cc_final: 0.8230 (ttmt) REVERT: B 138 ARG cc_start: 0.8260 (ttp-170) cc_final: 0.7746 (ttt90) REVERT: B 264 GLU cc_start: 0.6860 (tm-30) cc_final: 0.6588 (tm-30) REVERT: B 345 LEU cc_start: 0.5797 (OUTLIER) cc_final: 0.5555 (pp) REVERT: A 138 ARG cc_start: 0.8090 (ttt90) cc_final: 0.7871 (ttt90) REVERT: A 264 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7176 (mt-10) REVERT: A 345 LEU cc_start: 0.5755 (OUTLIER) cc_final: 0.5193 (tt) REVERT: C 12 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7964 (mttt) REVERT: C 242 HIS cc_start: 0.7484 (m-70) cc_final: 0.7121 (m-70) outliers start: 47 outliers final: 23 residues processed: 236 average time/residue: 1.0701 time to fit residues: 287.3207 Evaluate side-chains 226 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 193 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 204 LYS Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 300 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 3.9990 chunk 179 optimal weight: 0.0470 chunk 39 optimal weight: 0.0870 chunk 116 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 199 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1378 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= 0.226 Angle : 0.498 8.591 24135 Z= 0.260 Chirality : 0.046 0.191 2804 Planarity : 0.003 0.039 2986 Dihedral : 9.295 76.646 2687 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.58 % Allowed : 23.28 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.19), residues: 2094 helix: 0.64 (0.23), residues: 546 sheet: 0.97 (0.29), residues: 324 loop : 0.30 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 332 HIS 0.003 0.001 HIS B 337 PHE 0.017 0.002 PHE E 221 TYR 0.010 0.001 TYR F 225 ARG 0.004 0.000 ARG A 138 *********************** 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 243 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 197 time to evaluate : 1.995 Fit side-chains REVERT: F 21 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7938 (mt-10) REVERT: F 34 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8060 (ttpp) REVERT: F 103 SER cc_start: 0.8575 (OUTLIER) cc_final: 0.8194 (p) REVERT: F 204 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7165 (mmtm) REVERT: D 187 GLN cc_start: 0.7351 (mm-40) cc_final: 0.7123 (mm-40) REVERT: D 232 PHE cc_start: 0.7655 (OUTLIER) cc_final: 0.7400 (m-80) REVERT: D 245 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7596 (tt) REVERT: D 330 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.6076 (mpp) REVERT: E 16 ASP cc_start: 0.8243 (t0) cc_final: 0.7985 (t70) REVERT: E 21 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7673 (mt-10) REVERT: E 188 GLN cc_start: 0.7834 (tp40) cc_final: 0.7320 (tm-30) REVERT: E 264 GLU cc_start: 0.7326 (mm-30) cc_final: 0.6752 (mm-30) REVERT: B 138 ARG cc_start: 0.8253 (ttp-170) cc_final: 0.7741 (ttt90) REVERT: B 264 GLU cc_start: 0.6846 (tm-30) cc_final: 0.6547 (tm-30) REVERT: B 345 LEU cc_start: 0.5931 (OUTLIER) cc_final: 0.5681 (pp) REVERT: A 138 ARG cc_start: 0.8080 (ttt90) cc_final: 0.7880 (ttt90) REVERT: A 264 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7147 (mt-10) REVERT: A 345 LEU cc_start: 0.5668 (OUTLIER) cc_final: 0.5138 (tt) REVERT: C 12 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8004 (mttt) REVERT: C 242 HIS cc_start: 0.7525 (m-70) cc_final: 0.7123 (m-70) outliers start: 46 outliers final: 22 residues processed: 230 average time/residue: 1.1661 time to fit residues: 303.6816 Evaluate side-chains 228 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 195 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 204 LYS Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 300 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 136 ASN D 163 ASN C 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 17669 Z= 0.440 Angle : 0.595 8.593 24135 Z= 0.312 Chirality : 0.051 0.229 2804 Planarity : 0.004 0.040 2986 Dihedral : 9.514 77.289 2687 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.17 % Allowed : 22.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.19), residues: 2094 helix: 0.30 (0.22), residues: 540 sheet: 0.81 (0.28), residues: 354 loop : 0.13 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 332 HIS 0.004 0.001 HIS F 337 PHE 0.030 0.002 PHE E 221 TYR 0.014 0.002 TYR E 225 ARG 0.004 0.001 ARG D 90 *********************** 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 246 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 193 time to evaluate : 2.028 Fit side-chains REVERT: F 21 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7948 (mt-10) REVERT: F 34 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8273 (ttpp) REVERT: F 103 SER cc_start: 0.8602 (OUTLIER) cc_final: 0.8151 (p) REVERT: F 204 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7267 (mmtt) REVERT: F 224 ARG cc_start: 0.7496 (ttm170) cc_final: 0.7043 (ttm-80) REVERT: F 345 LEU cc_start: 0.4323 (OUTLIER) cc_final: 0.3408 (mp) REVERT: D 21 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7434 (mm-30) REVERT: D 199 ASN cc_start: 0.7668 (m-40) cc_final: 0.7316 (m-40) REVERT: D 232 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.7294 (m-80) REVERT: D 330 MET cc_start: 0.7051 (OUTLIER) cc_final: 0.6112 (mpp) REVERT: E 16 ASP cc_start: 0.8246 (t0) cc_final: 0.7999 (t70) REVERT: E 21 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7650 (mt-10) REVERT: E 188 GLN cc_start: 0.7848 (tp40) cc_final: 0.7340 (tm-30) REVERT: E 264 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6698 (mm-30) REVERT: B 264 GLU cc_start: 0.6732 (tm-30) cc_final: 0.6422 (tm-30) REVERT: B 345 LEU cc_start: 0.5880 (OUTLIER) cc_final: 0.5600 (pp) REVERT: A 188 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7491 (tp40) REVERT: A 264 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7143 (mt-10) REVERT: A 345 LEU cc_start: 0.5858 (OUTLIER) cc_final: 0.5296 (tp) REVERT: C 12 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8086 (mttt) REVERT: C 242 HIS cc_start: 0.7545 (m-70) cc_final: 0.7106 (m90) outliers start: 53 outliers final: 22 residues processed: 232 average time/residue: 1.2570 time to fit residues: 326.5103 Evaluate side-chains 221 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 186 time to evaluate : 1.886 ------------------------------------------------------------------------------- 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 103 SER Chi-restraints excluded: chain F residue 204 LYS Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain E residue 21 GLU 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 192 THR Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 328 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 118 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 156 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1492 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= 0.195 Angle : 0.493 8.728 24135 Z= 0.258 Chirality : 0.045 0.188 2804 Planarity : 0.003 0.036 2986 Dihedral : 9.226 74.930 2687 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.15 % Allowed : 23.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.19), residues: 2094 helix: 0.48 (0.23), residues: 546 sheet: 0.91 (0.29), residues: 324 loop : 0.21 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 332 HIS 0.004 0.001 HIS B 337 PHE 0.028 0.001 PHE E 221 TYR 0.010 0.001 TYR F 225 ARG 0.007 0.000 ARG A 138 *********************** 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 226 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 192 time to evaluate : 2.033 Fit side-chains REVERT: F 21 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7926 (mt-10) REVERT: F 204 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.7179 (mmtt) REVERT: F 224 ARG cc_start: 0.7480 (ttm170) cc_final: 0.7248 (ttm-80) REVERT: D 21 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7401 (mm-30) REVERT: D 330 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6038 (mpp) REVERT: E 16 ASP cc_start: 0.8239 (t0) cc_final: 0.7977 (t70) REVERT: E 188 GLN cc_start: 0.7850 (tp40) cc_final: 0.7359 (tm-30) REVERT: E 264 GLU cc_start: 0.7402 (mm-30) cc_final: 0.6809 (mm-30) REVERT: B 138 ARG cc_start: 0.8265 (ttp-170) cc_final: 0.7759 (ttt90) REVERT: B 264 GLU cc_start: 0.6863 (tm-30) cc_final: 0.6624 (tm-30) REVERT: B 345 LEU cc_start: 0.5929 (OUTLIER) cc_final: 0.5669 (pp) REVERT: A 56 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8463 (tt0) REVERT: A 220 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6969 (tp30) REVERT: A 264 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7107 (mt-10) REVERT: A 345 LEU cc_start: 0.5668 (OUTLIER) cc_final: 0.5135 (tp) REVERT: C 12 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.7988 (mttt) REVERT: C 232 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7610 (m-80) REVERT: C 242 HIS cc_start: 0.7550 (m-70) cc_final: 0.7152 (m90) outliers start: 34 outliers final: 17 residues processed: 215 average time/residue: 1.2283 time to fit residues: 296.1508 Evaluate side-chains 217 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 191 time to evaluate : 1.882 ------------------------------------------------------------------------------- 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 204 LYS Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 287 SER 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 232 PHE Chi-restraints excluded: chain C residue 300 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 0.5980 chunk 190 optimal weight: 0.1980 chunk 173 optimal weight: 3.9990 chunk 185 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1554 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= 0.190 Angle : 0.483 8.967 24135 Z= 0.253 Chirality : 0.045 0.193 2804 Planarity : 0.003 0.042 2986 Dihedral : 8.990 69.898 2687 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.94 % Allowed : 24.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.19), residues: 2094 helix: 0.63 (0.23), residues: 546 sheet: 0.99 (0.29), residues: 324 loop : 0.24 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 332 HIS 0.004 0.001 HIS B 337 PHE 0.028 0.001 PHE E 221 TYR 0.010 0.001 TYR F 225 ARG 0.008 0.000 ARG A 138 *********************** 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 225 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 196 time to evaluate : 1.931 Fit side-chains REVERT: F 21 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7896 (mt-10) REVERT: F 103 SER cc_start: 0.8573 (OUTLIER) cc_final: 0.8187 (p) REVERT: F 204 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.7120 (mmtm) REVERT: F 345 LEU cc_start: 0.4312 (OUTLIER) cc_final: 0.3504 (mt) REVERT: D 21 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7435 (mm-30) REVERT: D 187 GLN cc_start: 0.7352 (mm-40) cc_final: 0.7099 (mm-40) REVERT: D 330 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6071 (mpp) REVERT: E 16 ASP cc_start: 0.8210 (t0) cc_final: 0.7945 (t70) REVERT: E 188 GLN cc_start: 0.7849 (tp40) cc_final: 0.7353 (tm-30) REVERT: E 264 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7111 (tp30) REVERT: E 330 MET cc_start: 0.6870 (mmm) cc_final: 0.6171 (mmt) REVERT: B 34 LYS cc_start: 0.8463 (ttpt) cc_final: 0.8243 (ttmt) REVERT: B 138 ARG cc_start: 0.8252 (ttp-170) cc_final: 0.7744 (ttt90) REVERT: B 264 GLU cc_start: 0.6839 (tm-30) cc_final: 0.6537 (tm-30) REVERT: B 345 LEU cc_start: 0.5882 (OUTLIER) cc_final: 0.5624 (pp) REVERT: A 56 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8428 (tt0) REVERT: A 220 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6951 (tp30) REVERT: A 264 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7163 (mt-10) REVERT: A 345 LEU cc_start: 0.5496 (OUTLIER) cc_final: 0.5008 (tp) REVERT: C 12 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.7996 (mttt) REVERT: C 232 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7478 (m-80) REVERT: C 242 HIS cc_start: 0.7558 (m-70) cc_final: 0.7160 (m90) outliers start: 29 outliers final: 15 residues processed: 217 average time/residue: 1.1942 time to fit residues: 293.4955 Evaluate side-chains 217 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 191 time to evaluate : 1.873 ------------------------------------------------------------------------------- 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 204 LYS Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 330 MET 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 192 THR Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 287 SER 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 232 PHE Chi-restraints excluded: chain C residue 300 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 92 optimal weight: 0.0770 chunk 136 optimal weight: 0.1980 chunk 205 optimal weight: 10.0000 chunk 188 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 126 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 136 ASN ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 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 : 0.003 0.036 17669 Z= 0.202 Angle : 0.489 8.933 24135 Z= 0.256 Chirality : 0.046 0.200 2804 Planarity : 0.003 0.036 2986 Dihedral : 8.884 67.043 2687 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.88 % Allowed : 24.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.19), residues: 2094 helix: 0.60 (0.23), residues: 546 sheet: 1.01 (0.29), residues: 324 loop : 0.23 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 332 HIS 0.004 0.001 HIS B 337 PHE 0.029 0.002 PHE E 221 TYR 0.010 0.001 TYR C 225 ARG 0.007 0.000 ARG A 138 ********************** 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 214 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 186 time to evaluate : 2.004 Fit side-chains REVERT: F 21 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7913 (mt-10) REVERT: F 34 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7878 (tptt) REVERT: F 204 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.7118 (mmtm) REVERT: F 296 ASP cc_start: 0.8416 (t0) cc_final: 0.8180 (t0) REVERT: F 345 LEU cc_start: 0.4315 (OUTLIER) cc_final: 0.3524 (mt) REVERT: D 21 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7430 (mm-30) REVERT: D 187 GLN cc_start: 0.7344 (mm-40) cc_final: 0.7087 (mm-40) REVERT: D 330 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6108 (mpp) REVERT: E 16 ASP cc_start: 0.8201 (t0) cc_final: 0.7938 (t70) REVERT: E 188 GLN cc_start: 0.7844 (tp40) cc_final: 0.7327 (tm-30) REVERT: E 264 GLU cc_start: 0.7323 (mm-30) cc_final: 0.7106 (tp30) REVERT: E 330 MET cc_start: 0.6861 (mmm) cc_final: 0.6135 (mmt) REVERT: B 138 ARG cc_start: 0.8267 (ttp-170) cc_final: 0.7747 (ttt90) REVERT: B 264 GLU cc_start: 0.6848 (tm-30) cc_final: 0.6542 (tm-30) REVERT: B 345 LEU cc_start: 0.5922 (OUTLIER) cc_final: 0.5652 (pp) REVERT: A 56 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8453 (tt0) REVERT: A 220 GLU cc_start: 0.7381 (mt-10) cc_final: 0.6955 (tp30) REVERT: A 264 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7166 (mt-10) REVERT: A 345 LEU cc_start: 0.5510 (OUTLIER) cc_final: 0.5019 (tt) REVERT: C 12 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8006 (mttt) REVERT: C 232 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7553 (m-80) REVERT: C 242 HIS cc_start: 0.7524 (m-70) cc_final: 0.7131 (m90) outliers start: 28 outliers final: 15 residues processed: 208 average time/residue: 1.2066 time to fit residues: 282.1819 Evaluate side-chains 211 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 185 time to evaluate : 1.900 ------------------------------------------------------------------------------- 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 204 LYS Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 330 MET 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 192 THR Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 287 SER 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 232 PHE Chi-restraints excluded: chain C residue 300 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 0.0170 chunk 174 optimal weight: 0.0270 chunk 50 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 0.0670 chunk 163 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 30 optimal weight: 0.0870 overall best weight: 0.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 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 = 0.4047 r_free = 0.4047 target = 0.181232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.144125 restraints weight = 116893.427| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 5.16 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17669 Z= 0.104 Angle : 0.447 9.235 24135 Z= 0.234 Chirality : 0.044 0.181 2804 Planarity : 0.003 0.033 2986 Dihedral : 8.478 60.528 2687 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.18 % Allowed : 24.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.19), residues: 2094 helix: 0.98 (0.24), residues: 534 sheet: 1.07 (0.29), residues: 324 loop : 0.27 (0.19), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 332 HIS 0.004 0.001 HIS B 337 PHE 0.025 0.001 PHE E 221 TYR 0.008 0.001 TYR C 225 ARG 0.007 0.000 ARG A 138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5494.94 seconds wall clock time: 97 minutes 24.98 seconds (5844.98 seconds total)