Starting phenix.real_space_refine on Tue Aug 6 18:08:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud3_42145/08_2024/8ud3_42145.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud3_42145/08_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_42145/08_2024/8ud3_42145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud3_42145/08_2024/8ud3_42145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud3_42145/08_2024/8ud3_42145.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud3_42145/08_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 18.53, per 1000 atoms: 1.07 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: 7.11 Conformation dependent library (CDL) restraints added in 6.6 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: 6.92 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: 6.03 Time building geometry restraints manager: 7.77 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 3.040 nonbonded pdb=" O HIS D 242 " pdb=" OG SER D 287 " model vdw 2.223 3.040 nonbonded pdb=" O HIS E 242 " pdb=" OG SER E 287 " model vdw 2.245 3.040 nonbonded pdb=" O HIS C 242 " pdb=" OG SER C 287 " model vdw 2.245 3.040 nonbonded pdb=" NH1 ARG E 198 " pdb=" OE1 GLU E 210 " model vdw 2.251 3.120 ... (remaining 150689 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'B' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'C' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'D' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'E' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'F' and (resid 1 through 26 or resid 30 through 346)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.48 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 66.810 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 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:11.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.560 ------------------------------------------------------------------------------- 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 : 1.884 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: 1.2504 time to fit residues: 281.7569 Evaluate side-chains 181 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 176 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 328 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 0.2980 chunk 156 optimal weight: 0.0270 chunk 86 optimal weight: 0.0770 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 83 optimal weight: 0.2980 chunk 161 optimal weight: 0.0980 chunk 62 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 overall best weight: 0.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 HIS C 14 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17669 Z= 0.125 Angle : 0.496 9.040 24135 Z= 0.260 Chirality : 0.045 0.165 2804 Planarity : 0.003 0.060 2986 Dihedral : 9.976 81.655 2693 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.20 % Allowed : 22.26 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.19), residues: 2094 helix: 0.79 (0.23), residues: 540 sheet: 0.93 (0.29), residues: 312 loop : 0.38 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 332 HIS 0.009 0.001 HIS A 337 PHE 0.009 0.001 PHE D 7 TYR 0.009 0.001 TYR F 225 ARG 0.005 0.000 ARG E 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 205 time to evaluate : 2.046 Fit side-chains REVERT: F 187 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7366 (mt0) REVERT: D 41 GLU cc_start: 0.8221 (tt0) cc_final: 0.8001 (tt0) REVERT: E 16 ASP cc_start: 0.8148 (t0) cc_final: 0.7888 (t70) REVERT: E 191 GLU cc_start: 0.7102 (tp30) cc_final: 0.6600 (tm-30) REVERT: E 199 ASN cc_start: 0.7604 (m-40) cc_final: 0.6900 (t0) REVERT: E 220 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.6094 (mp0) REVERT: E 241 SER cc_start: 0.8676 (m) cc_final: 0.8459 (m) REVERT: B 138 ARG cc_start: 0.8233 (ttp-170) cc_final: 0.7763 (ttt90) REVERT: B 264 GLU cc_start: 0.6835 (tm-30) cc_final: 0.6513 (tm-30) REVERT: B 345 LEU cc_start: 0.6085 (OUTLIER) cc_final: 0.5864 (pp) REVERT: A 19 GLN cc_start: 0.8328 (mm-40) cc_final: 0.8047 (mp10) REVERT: A 264 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7126 (mt-10) REVERT: A 345 LEU cc_start: 0.5981 (OUTLIER) cc_final: 0.5236 (tt) REVERT: C 138 ARG cc_start: 0.8007 (tpt-90) cc_final: 0.7321 (ttp-170) REVERT: C 306 ILE cc_start: 0.7221 (tt) cc_final: 0.6718 (pt) outliers start: 41 outliers final: 7 residues processed: 234 average time/residue: 1.1276 time to fit residues: 299.1285 Evaluate side-chains 190 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 179 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 1.9990 chunk 58 optimal weight: 0.0870 chunk 155 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 202 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 185 optimal weight: 0.1980 chunk 63 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 277 ASN A 337 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1250 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= 0.180 Angle : 0.500 11.755 24135 Z= 0.260 Chirality : 0.045 0.166 2804 Planarity : 0.003 0.053 2986 Dihedral : 9.487 79.932 2686 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.83 % Allowed : 23.23 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.19), residues: 2094 helix: 0.78 (0.23), residues: 540 sheet: 1.03 (0.29), residues: 312 loop : 0.35 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 332 HIS 0.009 0.001 HIS A 337 PHE 0.013 0.001 PHE E 263 TYR 0.012 0.001 TYR F 225 ARG 0.009 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 227 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 193 time to evaluate : 1.787 Fit side-chains REVERT: F 187 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7387 (mt0) REVERT: F 224 ARG cc_start: 0.7579 (ttm170) cc_final: 0.6911 (ttm-80) REVERT: D 21 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7436 (mt-10) REVERT: D 187 GLN cc_start: 0.7330 (mm-40) cc_final: 0.7107 (mm-40) REVERT: D 232 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.7333 (m-80) REVERT: D 245 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7504 (tt) REVERT: D 330 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.6876 (mmp) REVERT: E 16 ASP cc_start: 0.8203 (t0) cc_final: 0.7952 (t70) REVERT: E 191 GLU cc_start: 0.7050 (tp30) cc_final: 0.6602 (tm-30) REVERT: E 241 SER cc_start: 0.8780 (m) cc_final: 0.8577 (m) REVERT: E 263 PHE cc_start: 0.8225 (p90) cc_final: 0.7945 (p90) REVERT: E 264 GLU cc_start: 0.7227 (mm-30) cc_final: 0.6712 (mm-30) REVERT: B 34 LYS cc_start: 0.8387 (ttpt) cc_final: 0.8164 (ttmt) REVERT: B 138 ARG cc_start: 0.8213 (ttp-170) cc_final: 0.7721 (ttt90) REVERT: B 264 GLU cc_start: 0.6813 (tm-30) cc_final: 0.6456 (tm-30) REVERT: B 345 LEU cc_start: 0.6106 (OUTLIER) cc_final: 0.5883 (pp) REVERT: A 264 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7112 (mt-10) REVERT: A 345 LEU cc_start: 0.5695 (OUTLIER) cc_final: 0.5009 (tt) REVERT: C 12 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.7991 (mtpt) REVERT: C 138 ARG cc_start: 0.7990 (tpt-90) cc_final: 0.7328 (ttp-170) REVERT: C 306 ILE cc_start: 0.7223 (tt) cc_final: 0.6724 (pt) outliers start: 34 outliers final: 9 residues processed: 216 average time/residue: 1.1610 time to fit residues: 283.7681 Evaluate side-chains 203 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 186 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain 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 345 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 0.4980 chunk 140 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 188 optimal weight: 0.6980 chunk 199 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 163 ASN C 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17669 Z= 0.320 Angle : 0.553 9.564 24135 Z= 0.287 Chirality : 0.048 0.186 2804 Planarity : 0.004 0.048 2986 Dihedral : 9.519 78.619 2686 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.42 % Allowed : 22.96 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.19), residues: 2094 helix: 0.53 (0.23), residues: 540 sheet: 0.81 (0.28), residues: 354 loop : 0.20 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 332 HIS 0.003 0.001 HIS B 337 PHE 0.014 0.002 PHE C 329 TYR 0.012 0.002 TYR E 32 ARG 0.008 0.001 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 227 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 184 time to evaluate : 1.965 Fit side-chains REVERT: F 103 SER cc_start: 0.8578 (OUTLIER) cc_final: 0.8124 (p) REVERT: F 136 ASN cc_start: 0.7750 (m110) cc_final: 0.7462 (m-40) REVERT: F 187 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7351 (mt0) REVERT: F 224 ARG cc_start: 0.7544 (ttm170) cc_final: 0.6862 (ttm-80) REVERT: D 12 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7867 (mttm) REVERT: D 21 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7434 (mt-10) REVERT: D 199 ASN cc_start: 0.7461 (m-40) cc_final: 0.7099 (m110) REVERT: D 232 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.7329 (m-80) REVERT: D 245 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7636 (tt) REVERT: D 330 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6898 (mmp) REVERT: E 16 ASP cc_start: 0.8203 (t0) cc_final: 0.7946 (t70) REVERT: E 263 PHE cc_start: 0.8358 (p90) cc_final: 0.8072 (p90) REVERT: E 264 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6675 (mm-30) REVERT: B 264 GLU cc_start: 0.6887 (tm-30) cc_final: 0.6578 (tm-30) REVERT: B 344 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6995 (tmtt) REVERT: B 345 LEU cc_start: 0.6033 (OUTLIER) cc_final: 0.5709 (pp) REVERT: A 264 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7177 (mt-10) REVERT: A 284 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.6884 (tm-30) REVERT: A 345 LEU cc_start: 0.5872 (OUTLIER) cc_final: 0.5197 (tt) REVERT: A 346 GLN cc_start: 0.4790 (OUTLIER) cc_final: 0.3645 (tm-30) REVERT: C 138 ARG cc_start: 0.7988 (tpt-90) cc_final: 0.7294 (ttp-170) REVERT: C 188 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8000 (tm-30) outliers start: 43 outliers final: 14 residues processed: 214 average time/residue: 1.3034 time to fit residues: 313.8792 Evaluate side-chains 200 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 173 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain C residue 328 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 2.9990 chunk 113 optimal weight: 0.0040 chunk 2 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1419 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= 0.207 Angle : 0.500 9.336 24135 Z= 0.260 Chirality : 0.046 0.189 2804 Planarity : 0.003 0.043 2986 Dihedral : 9.327 77.014 2686 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.83 % Allowed : 23.60 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.19), residues: 2094 helix: 0.63 (0.23), residues: 540 sheet: 0.82 (0.28), residues: 354 loop : 0.20 (0.19), residues: 1200 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 0.013 0.001 PHE F 329 TYR 0.010 0.001 TYR F 225 ARG 0.009 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 220 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 188 time to evaluate : 2.488 Fit side-chains REVERT: F 136 ASN cc_start: 0.7746 (m110) cc_final: 0.7478 (m-40) REVERT: F 187 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7345 (mt0) REVERT: F 232 PHE cc_start: 0.7616 (m-80) cc_final: 0.7264 (m-80) REVERT: D 21 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7423 (mt-10) REVERT: D 187 GLN cc_start: 0.7354 (mm-40) cc_final: 0.7148 (mm-40) REVERT: D 199 ASN cc_start: 0.7362 (m-40) cc_final: 0.7041 (m110) REVERT: D 232 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.7335 (m-80) REVERT: D 245 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7548 (tt) REVERT: D 265 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7785 (mt) REVERT: E 16 ASP cc_start: 0.8158 (t0) cc_final: 0.7912 (t70) REVERT: E 263 PHE cc_start: 0.8353 (p90) cc_final: 0.8001 (p90) REVERT: E 264 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6647 (mm-30) REVERT: B 264 GLU cc_start: 0.6892 (tm-30) cc_final: 0.6643 (tm-30) REVERT: B 344 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.7011 (tmtt) REVERT: B 345 LEU cc_start: 0.6005 (OUTLIER) cc_final: 0.5692 (pp) REVERT: A 19 GLN cc_start: 0.8318 (mm-40) cc_final: 0.8056 (mp10) REVERT: A 264 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7165 (mt-10) REVERT: A 346 GLN cc_start: 0.4646 (OUTLIER) cc_final: 0.3688 (tm-30) REVERT: C 138 ARG cc_start: 0.7998 (tpt-90) cc_final: 0.7291 (ttp-170) REVERT: C 188 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7976 (tm-30) REVERT: C 306 ILE cc_start: 0.7270 (tt) cc_final: 0.6727 (pt) outliers start: 32 outliers final: 14 residues processed: 211 average time/residue: 1.1635 time to fit residues: 278.5204 Evaluate side-chains 204 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 181 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 265 LEU 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 344 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 188 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 0.5980 chunk 179 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 199 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17669 Z= 0.226 Angle : 0.504 9.185 24135 Z= 0.263 Chirality : 0.046 0.185 2804 Planarity : 0.003 0.043 2986 Dihedral : 9.259 75.695 2684 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.37 % Allowed : 23.06 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.19), residues: 2094 helix: 0.61 (0.23), residues: 540 sheet: 0.86 (0.28), residues: 354 loop : 0.17 (0.19), residues: 1200 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 0.012 0.002 PHE E 268 TYR 0.010 0.001 TYR E 225 ARG 0.009 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 227 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 185 time to evaluate : 2.535 Fit side-chains revert: symmetry clash REVERT: F 34 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8020 (ttpp) REVERT: F 103 SER cc_start: 0.8553 (OUTLIER) cc_final: 0.8117 (p) REVERT: F 136 ASN cc_start: 0.7750 (m110) cc_final: 0.7472 (m-40) REVERT: F 187 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7396 (mt0) REVERT: F 232 PHE cc_start: 0.7662 (m-80) cc_final: 0.7285 (m-80) REVERT: D 21 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7410 (mt-10) REVERT: D 187 GLN cc_start: 0.7388 (mm-40) cc_final: 0.7169 (mm-40) REVERT: D 199 ASN cc_start: 0.7423 (m-40) cc_final: 0.7115 (m110) REVERT: D 232 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.7368 (m-80) REVERT: D 245 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7567 (tt) REVERT: E 16 ASP cc_start: 0.8166 (t0) cc_final: 0.7896 (t70) REVERT: E 263 PHE cc_start: 0.8348 (p90) cc_final: 0.8011 (p90) REVERT: E 264 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6664 (mm-30) REVERT: B 109 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8453 (mppt) REVERT: B 138 ARG cc_start: 0.8219 (ttp-170) cc_final: 0.7714 (ttt90) REVERT: B 264 GLU cc_start: 0.6875 (tm-30) cc_final: 0.6599 (tm-30) REVERT: B 344 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6983 (tmtt) REVERT: B 345 LEU cc_start: 0.5901 (OUTLIER) cc_final: 0.5538 (pp) REVERT: A 264 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7181 (mt-10) REVERT: A 284 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.6855 (tm-30) REVERT: A 346 GLN cc_start: 0.4700 (OUTLIER) cc_final: 0.3581 (tm-30) REVERT: C 12 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8020 (mtpt) REVERT: C 110 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8556 (mtmt) REVERT: C 138 ARG cc_start: 0.7986 (tpt-90) cc_final: 0.7289 (ttp-170) outliers start: 42 outliers final: 15 residues processed: 216 average time/residue: 1.1630 time to fit residues: 283.6442 Evaluate side-chains 211 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 183 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 328 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 167 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17669 Z= 0.349 Angle : 0.557 8.716 24135 Z= 0.291 Chirality : 0.049 0.205 2804 Planarity : 0.004 0.049 2986 Dihedral : 9.347 75.051 2684 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.58 % Allowed : 22.74 % 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: 0.42 (0.19), residues: 2094 helix: 0.43 (0.23), residues: 534 sheet: 1.00 (0.29), residues: 342 loop : 0.09 (0.19), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 332 HIS 0.003 0.001 HIS B 337 PHE 0.020 0.002 PHE E 221 TYR 0.013 0.002 TYR E 225 ARG 0.008 0.001 ARG A 138 *********************** 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 233 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 187 time to evaluate : 1.955 Fit side-chains REVERT: F 21 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: F 34 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8213 (ttpp) REVERT: F 103 SER cc_start: 0.8637 (OUTLIER) cc_final: 0.8168 (p) REVERT: F 136 ASN cc_start: 0.7755 (m110) cc_final: 0.7487 (m-40) REVERT: F 187 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7387 (mt0) REVERT: F 204 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7200 (mmtt) REVERT: F 224 ARG cc_start: 0.7533 (ttm170) cc_final: 0.7268 (ttm-80) REVERT: D 21 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7436 (mt-10) REVERT: D 199 ASN cc_start: 0.7525 (m-40) cc_final: 0.7185 (m110) REVERT: D 232 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.7308 (m-80) REVERT: D 245 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7639 (tt) REVERT: D 330 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6153 (mpp) REVERT: E 16 ASP cc_start: 0.8191 (t0) cc_final: 0.7928 (t70) REVERT: E 263 PHE cc_start: 0.8390 (p90) cc_final: 0.8077 (p90) REVERT: E 264 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6718 (mm-30) REVERT: B 264 GLU cc_start: 0.6717 (tm-30) cc_final: 0.6406 (tm-30) REVERT: B 344 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.7099 (tmtt) REVERT: B 345 LEU cc_start: 0.5901 (OUTLIER) cc_final: 0.5539 (pp) REVERT: A 264 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7114 (mt-10) REVERT: A 284 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.6775 (tm-30) REVERT: C 110 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8566 (mtmt) REVERT: C 138 ARG cc_start: 0.7997 (tpt-90) cc_final: 0.7282 (ttp-170) REVERT: C 188 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8107 (tm-30) outliers start: 46 outliers final: 18 residues processed: 219 average time/residue: 1.2793 time to fit residues: 313.2006 Evaluate side-chains 216 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 184 time to evaluate : 1.957 ------------------------------------------------------------------------------- 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 187 GLN Chi-restraints excluded: chain F residue 204 LYS Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain C residue 328 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 0.2980 chunk 79 optimal weight: 0.7980 chunk 118 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 38 optimal weight: 0.2980 chunk 126 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 156 optimal weight: 0.8980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17669 Z= 0.143 Angle : 0.472 8.904 24135 Z= 0.248 Chirality : 0.044 0.178 2804 Planarity : 0.003 0.036 2986 Dihedral : 9.003 71.487 2684 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.67 % Allowed : 23.76 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.19), residues: 2094 helix: 0.66 (0.23), residues: 540 sheet: 0.99 (0.29), residues: 324 loop : 0.17 (0.19), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 332 HIS 0.004 0.001 HIS B 337 PHE 0.023 0.001 PHE E 221 TYR 0.009 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 232 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 203 time to evaluate : 2.091 Fit side-chains REVERT: F 136 ASN cc_start: 0.7725 (m110) cc_final: 0.7443 (m-40) REVERT: F 224 ARG cc_start: 0.7504 (ttm170) cc_final: 0.6920 (ttm-80) REVERT: F 232 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.7274 (m-80) REVERT: D 21 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7338 (mt-10) REVERT: D 41 GLU cc_start: 0.8241 (tt0) cc_final: 0.8021 (tt0) REVERT: D 187 GLN cc_start: 0.7332 (mm-40) cc_final: 0.7106 (mm-40) REVERT: D 199 ASN cc_start: 0.7336 (m-40) cc_final: 0.7121 (m110) REVERT: D 330 MET cc_start: 0.7033 (OUTLIER) cc_final: 0.6010 (mpp) REVERT: E 16 ASP cc_start: 0.8116 (t0) cc_final: 0.7836 (t70) REVERT: E 263 PHE cc_start: 0.8306 (p90) cc_final: 0.7914 (p90) REVERT: E 264 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6681 (mm-30) REVERT: B 34 LYS cc_start: 0.8385 (ttpt) cc_final: 0.8151 (ttmt) REVERT: B 138 ARG cc_start: 0.8210 (ttp-170) cc_final: 0.7694 (ttt90) REVERT: B 199 ASN cc_start: 0.7504 (m-40) cc_final: 0.7172 (t0) REVERT: B 264 GLU cc_start: 0.6891 (tm-30) cc_final: 0.6595 (tm-30) REVERT: B 344 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.7017 (tmtt) REVERT: B 345 LEU cc_start: 0.5886 (OUTLIER) cc_final: 0.5525 (pp) REVERT: A 264 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7142 (mt-10) REVERT: C 110 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8544 (mtmt) REVERT: C 138 ARG cc_start: 0.7962 (tpt-90) cc_final: 0.7303 (ttp-170) outliers start: 29 outliers final: 12 residues processed: 224 average time/residue: 1.2167 time to fit residues: 306.2823 Evaluate side-chains 208 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 190 time to evaluate : 1.948 ------------------------------------------------------------------------------- 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 232 PHE Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 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 344 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 147 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 0.5980 chunk 190 optimal weight: 0.4980 chunk 173 optimal weight: 0.7980 chunk 185 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 174 optimal weight: 0.5980 chunk 184 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1690 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= 0.187 Angle : 0.485 8.833 24135 Z= 0.254 Chirality : 0.045 0.182 2804 Planarity : 0.003 0.036 2986 Dihedral : 8.861 67.840 2684 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.34 % Allowed : 24.09 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.19), residues: 2094 helix: 0.71 (0.23), residues: 540 sheet: 0.96 (0.29), residues: 354 loop : 0.17 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 332 HIS 0.004 0.001 HIS B 337 PHE 0.025 0.001 PHE E 221 TYR 0.010 0.001 TYR F 225 ARG 0.007 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 219 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 196 time to evaluate : 2.441 Fit side-chains REVERT: F 136 ASN cc_start: 0.7734 (m110) cc_final: 0.7456 (m-40) REVERT: F 224 ARG cc_start: 0.7494 (ttm170) cc_final: 0.7280 (ttm-80) REVERT: F 232 PHE cc_start: 0.7609 (m-80) cc_final: 0.7285 (m-80) REVERT: F 345 LEU cc_start: 0.4212 (OUTLIER) cc_final: 0.3307 (mt) REVERT: D 21 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7377 (mt-10) REVERT: D 187 GLN cc_start: 0.7353 (mm-40) cc_final: 0.7123 (mm-40) REVERT: D 199 ASN cc_start: 0.7416 (m-40) cc_final: 0.7197 (m110) REVERT: D 245 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7498 (tt) REVERT: D 330 MET cc_start: 0.7028 (OUTLIER) cc_final: 0.6019 (mpp) REVERT: E 16 ASP cc_start: 0.8132 (t0) cc_final: 0.7855 (t70) REVERT: E 263 PHE cc_start: 0.8331 (p90) cc_final: 0.7991 (p90) REVERT: E 264 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6657 (mm-30) REVERT: E 330 MET cc_start: 0.6892 (mmm) cc_final: 0.6158 (mmt) REVERT: B 34 LYS cc_start: 0.8415 (ttpt) cc_final: 0.8181 (ttmt) REVERT: B 138 ARG cc_start: 0.8230 (ttp-170) cc_final: 0.7711 (ttt90) REVERT: B 199 ASN cc_start: 0.7561 (m-40) cc_final: 0.7230 (t0) REVERT: B 264 GLU cc_start: 0.6852 (tm-30) cc_final: 0.6547 (tm-30) REVERT: B 344 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6943 (tmtt) REVERT: B 345 LEU cc_start: 0.5815 (OUTLIER) cc_final: 0.5446 (pp) REVERT: A 264 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7136 (mt-10) REVERT: C 110 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8541 (mtmt) REVERT: C 138 ARG cc_start: 0.7954 (tpt-90) cc_final: 0.7294 (ttp-170) outliers start: 23 outliers final: 15 residues processed: 212 average time/residue: 1.2486 time to fit residues: 300.0727 Evaluate side-chains 215 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 193 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 250 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 0.0670 chunk 195 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 136 optimal weight: 0.4980 chunk 205 optimal weight: 10.0000 chunk 188 optimal weight: 0.1980 chunk 163 optimal weight: 0.0980 chunk 16 optimal weight: 0.9990 chunk 126 optimal weight: 0.0060 chunk 100 optimal weight: 3.9990 overall best weight: 0.1734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17669 Z= 0.115 Angle : 0.461 8.992 24135 Z= 0.241 Chirality : 0.044 0.174 2804 Planarity : 0.003 0.035 2986 Dihedral : 8.566 63.149 2684 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.18 % Allowed : 24.35 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.19), residues: 2094 helix: 0.85 (0.23), residues: 540 sheet: 1.19 (0.30), residues: 312 loop : 0.26 (0.19), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 332 HIS 0.004 0.001 HIS B 337 PHE 0.022 0.001 PHE E 221 TYR 0.008 0.001 TYR C 278 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 223 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 203 time to evaluate : 2.057 Fit side-chains revert: symmetry clash REVERT: F 136 ASN cc_start: 0.7685 (m110) cc_final: 0.7413 (m-40) REVERT: F 345 LEU cc_start: 0.4169 (OUTLIER) cc_final: 0.3299 (mt) REVERT: D 21 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7289 (mm-30) REVERT: D 187 GLN cc_start: 0.7269 (mm-40) cc_final: 0.7050 (mm-40) REVERT: D 245 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7479 (tt) REVERT: D 330 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.5970 (mpp) REVERT: E 16 ASP cc_start: 0.8129 (t0) cc_final: 0.7842 (t70) REVERT: E 56 GLU cc_start: 0.8002 (tt0) cc_final: 0.7634 (tt0) REVERT: E 263 PHE cc_start: 0.8315 (p90) cc_final: 0.7979 (p90) REVERT: E 264 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6681 (mm-30) REVERT: E 330 MET cc_start: 0.6962 (mmm) cc_final: 0.6196 (mmt) REVERT: B 138 ARG cc_start: 0.8215 (ttp-170) cc_final: 0.7697 (ttt90) REVERT: B 199 ASN cc_start: 0.7501 (m-40) cc_final: 0.7205 (t0) REVERT: B 264 GLU cc_start: 0.6789 (tm-30) cc_final: 0.6498 (tm-30) REVERT: A 264 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7114 (mt-10) REVERT: C 138 ARG cc_start: 0.7943 (tpt-90) cc_final: 0.7343 (ttp-170) REVERT: C 264 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7172 (mt-10) outliers start: 20 outliers final: 11 residues processed: 217 average time/residue: 1.1403 time to fit residues: 280.7071 Evaluate side-chains 204 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 189 time to evaluate : 1.892 ------------------------------------------------------------------------------- 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 264 GLU Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 340 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 45 optimal weight: 0.0370 chunk 163 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 168 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 30 optimal weight: 0.1980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.171000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.131625 restraints weight = 113359.873| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 5.79 r_work: 0.2833 rms_B_bonded: 5.41 restraints_weight: 2.0000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17669 Z= 0.148 Angle : 0.476 12.337 24135 Z= 0.246 Chirality : 0.045 0.181 2804 Planarity : 0.003 0.044 2986 Dihedral : 8.521 59.767 2684 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.08 % Allowed : 24.41 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.19), residues: 2094 helix: 0.79 (0.23), residues: 546 sheet: 1.26 (0.30), residues: 312 loop : 0.31 (0.19), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 332 HIS 0.004 0.001 HIS B 337 PHE 0.026 0.001 PHE E 221 TYR 0.009 0.001 TYR F 225 ARG 0.009 0.000 ARG A 138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5823.93 seconds wall clock time: 103 minutes 10.17 seconds (6190.17 seconds total)