Starting phenix.real_space_refine on Mon Jul 22 07:31:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud4_42146/07_2024/8ud4_42146.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud4_42146/07_2024/8ud4_42146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud4_42146/07_2024/8ud4_42146.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud4_42146/07_2024/8ud4_42146.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud4_42146/07_2024/8ud4_42146.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud4_42146/07_2024/8ud4_42146.cif" } resolution = 3.25 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= 0.030 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 46 5.49 5 S 60 5.16 5 C 11057 2.51 5 N 2851 2.21 5 O 3484 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 113": "OE1" <-> "OE2" Residue "F GLU 228": "OE1" <-> "OE2" Residue "F GLU 326": "OE1" <-> "OE2" Residue "D PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D GLU 228": "OE1" <-> "OE2" Residue "D GLU 264": "OE1" <-> "OE2" Residue "D PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 326": "OE1" <-> "OE2" Residue "E PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E GLU 145": "OE1" <-> "OE2" Residue "E TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 215": "OE1" <-> "OE2" Residue "E GLU 223": "OE1" <-> "OE2" Residue "E GLU 228": "OE1" <-> "OE2" Residue "E PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B GLU 220": "OE1" <-> "OE2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "B GLU 326": "OE1" <-> "OE2" Residue "A GLU 3": "OE1" <-> "OE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "C GLU 3": "OE1" <-> "OE2" Residue "C GLU 21": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C GLU 260": "OE1" <-> "OE2" Residue "C GLU 326": "OE1" <-> "OE2" Residue "C GLU 339": "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: 17498 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: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 463 Classifications: {'RNA': 23} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 22} Link IDs: {'rna3p': 22} Chain: "H" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 505 Classifications: {'RNA': 23} Modifications used: {'rna3p_pur': 22, 'rna3p_pyr': 1} Link IDs: {'rna3p': 22} 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: 16.92, per 1000 atoms: 0.97 Number of scatterers: 17498 At special positions: 0 Unit cell: (115.92, 123.28, 135.24, 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 46 15.00 O 3484 8.00 N 2851 7.00 C 11057 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: 6.88 Conformation dependent library (CDL) restraints added in 5.4 seconds 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3924 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 44 sheets defined 26.2% alpha, 23.0% beta 21 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 6.43 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: 3.651A 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 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 Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.585A 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 226 removed outlier: 3.566A pdb=" N PHE E 221 " --> pdb=" O ALA E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 236 removed outlier: 3.660A pdb=" N VAL E 236 " --> pdb=" O PHE E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 261 removed outlier: 3.535A 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 129 through 137 removed outlier: 3.596A pdb=" N LEU B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) 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 removed outlier: 3.584A pdb=" N VAL B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.584A 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 removed outlier: 3.681A pdb=" N VAL A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) 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 129 through 137 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 removed outlier: 3.587A pdb=" N VAL C 236 " --> pdb=" O PHE C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.599A 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: 6.685A pdb=" N VAL F 31 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 106 through 108 removed outlier: 8.281A pdb=" N THR F 98 " --> pdb=" O ILE F 107 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE F 99 " --> pdb=" O ALA F 80 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ASP F 124 " --> pdb=" O ALA F 81 " (cutoff:3.500A) removed outlier: 4.675A 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 160 through 162 Processing sheet with id=AA5, first strand: chain 'F' and resid 263 through 266 removed outlier: 3.525A pdb=" N GLU F 266 " --> pdb=" O PHE F 279 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ILE F 280 " --> pdb=" O CYS F 290 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N CYS F 290 " --> pdb=" O ILE F 280 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASP F 282 " --> pdb=" O SER F 288 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N SER F 288 " --> pdb=" O ASP F 282 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 315 through 322 removed outlier: 7.388A pdb=" N SER F 328 " --> pdb=" O PRO F 343 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N MET F 330 " --> pdb=" O PHE F 341 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE F 341 " --> pdb=" O MET F 330 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP F 332 " --> pdb=" O GLU F 339 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 24 through 27 removed outlier: 6.669A pdb=" N VAL D 31 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 79 through 80 removed outlier: 7.121A pdb=" N ILE D 79 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ASP D 124 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 79 through 80 removed outlier: 7.121A pdb=" N ILE D 79 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ASP D 124 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 86 through 87 Processing sheet with id=AB2, first strand: chain 'D' and resid 160 through 162 Processing sheet with id=AB3, first strand: chain 'D' and resid 263 through 266 removed outlier: 3.579A pdb=" N GLU D 266 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ILE D 280 " --> pdb=" O CYS D 290 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N CYS D 290 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP D 282 " --> pdb=" O SER D 288 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N SER D 288 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 315 through 322 removed outlier: 7.483A pdb=" N SER D 328 " --> pdb=" O PRO D 343 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N MET D 330 " --> pdb=" O PHE D 341 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N PHE D 341 " --> pdb=" O MET D 330 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N TRP D 332 " --> pdb=" O GLU D 339 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 24 through 27 removed outlier: 6.668A pdb=" N VAL E 31 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.397A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N ASP E 124 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS E 180 " --> pdb=" O GLN E 187 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AB8, first strand: chain 'E' and resid 98 through 99 removed outlier: 8.157A pdb=" N THR E 98 " --> pdb=" O ILE E 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 160 through 162 Processing sheet with id=AC1, first strand: chain 'E' and resid 264 through 266 removed outlier: 4.873A pdb=" N ILE E 280 " --> pdb=" O CYS E 290 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N CYS E 290 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 315 through 322 removed outlier: 7.345A pdb=" N SER E 328 " --> pdb=" O PRO E 343 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET E 330 " --> pdb=" O PHE E 341 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE E 341 " --> pdb=" O MET E 330 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TRP E 332 " --> pdb=" O GLU E 339 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 24 through 27 removed outlier: 6.732A pdb=" N VAL B 31 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.268A pdb=" N ILE B 79 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N ASP B 124 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS B 180 " --> pdb=" O GLN B 187 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AC6, first strand: chain 'B' and resid 98 through 99 removed outlier: 8.227A pdb=" N THR B 98 " --> pdb=" O ILE B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AC8, first strand: chain 'B' and resid 264 through 266 removed outlier: 3.583A pdb=" N GLU B 266 " --> pdb=" O PHE B 279 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 275 through 277 Processing sheet with id=AD1, first strand: chain 'B' and resid 315 through 322 removed outlier: 7.221A pdb=" N SER B 328 " --> pdb=" O PRO B 343 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N MET B 330 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE B 341 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP B 332 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 24 through 27 removed outlier: 6.717A pdb=" N VAL A 31 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.022A pdb=" N ILE A 79 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N ASP A 124 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.022A pdb=" N ILE A 79 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N ASP A 124 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS A 180 " --> pdb=" O GLN A 187 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AD6, first strand: chain 'A' and resid 98 through 99 removed outlier: 8.372A pdb=" N THR A 98 " --> pdb=" O ILE A 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AD8, first strand: chain 'A' and resid 264 through 266 removed outlier: 4.997A pdb=" N ILE A 280 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N CYS A 290 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 316 through 322 removed outlier: 3.515A pdb=" N TYR A 342 " --> pdb=" O MET A 330 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 24 through 27 removed outlier: 6.717A pdb=" N VAL C 31 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.156A pdb=" N ILE C 79 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N ASP C 124 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.156A pdb=" N ILE C 79 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N ASP C 124 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LYS C 180 " --> pdb=" O GLN C 187 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AE5, first strand: chain 'C' and resid 98 through 99 removed outlier: 8.144A pdb=" N THR C 98 " --> pdb=" O ILE C 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 160 through 162 Processing sheet with id=AE7, first strand: chain 'C' and resid 264 through 266 removed outlier: 3.529A pdb=" N GLU C 264 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ILE C 280 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N CYS C 290 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 315 through 322 removed outlier: 3.603A pdb=" N THR C 340 " --> pdb=" O TRP C 332 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL C 338 " --> pdb=" O LYS C 334 " (cutoff:3.500A) 621 hydrogen bonds defined for protein. 1611 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 5.79 Time building geometry restraints manager: 7.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3000 1.32 - 1.44: 4734 1.44 - 1.57: 10038 1.57 - 1.69: 91 1.69 - 1.81: 90 Bond restraints: 17953 Sorted by residual: bond pdb=" CA LYS C 149 " pdb=" C LYS C 149 " ideal model delta sigma weight residual 1.524 1.490 0.035 1.22e-02 6.72e+03 8.08e+00 bond pdb=" C THR D 98 " pdb=" O THR D 98 " ideal model delta sigma weight residual 1.235 1.201 0.034 1.26e-02 6.30e+03 7.49e+00 bond pdb=" C ILE D 99 " pdb=" O ILE D 99 " ideal model delta sigma weight residual 1.236 1.208 0.028 1.19e-02 7.06e+03 5.43e+00 bond pdb=" CA ILE D 99 " pdb=" CB ILE D 99 " ideal model delta sigma weight residual 1.540 1.511 0.029 1.36e-02 5.41e+03 4.60e+00 bond pdb=" CA VAL C 148 " pdb=" C VAL C 148 " ideal model delta sigma weight residual 1.524 1.496 0.027 1.28e-02 6.10e+03 4.52e+00 ... (remaining 17948 not shown) Histogram of bond angle deviations from ideal: 97.46 - 104.76: 434 104.76 - 112.07: 9056 112.07 - 119.37: 5964 119.37 - 126.68: 8813 126.68 - 133.98: 310 Bond angle restraints: 24577 Sorted by residual: angle pdb=" N LYS C 149 " pdb=" CA LYS C 149 " pdb=" C LYS C 149 " ideal model delta sigma weight residual 108.96 116.67 -7.71 1.59e+00 3.96e-01 2.35e+01 angle pdb=" C4' A H 5 " pdb=" C3' A H 5 " pdb=" O3' A H 5 " ideal model delta sigma weight residual 113.00 106.84 6.16 1.50e+00 4.44e-01 1.69e+01 angle pdb=" N LYS D 89 " pdb=" CA LYS D 89 " pdb=" C LYS D 89 " ideal model delta sigma weight residual 113.20 108.24 4.96 1.21e+00 6.83e-01 1.68e+01 angle pdb=" C LYS D 344 " pdb=" N LEU D 345 " pdb=" CA LEU D 345 " ideal model delta sigma weight residual 121.54 129.05 -7.51 1.91e+00 2.74e-01 1.55e+01 angle pdb=" C LYS C 344 " pdb=" N LEU C 345 " pdb=" CA LEU C 345 " ideal model delta sigma weight residual 121.54 129.02 -7.48 1.91e+00 2.74e-01 1.53e+01 ... (remaining 24572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.33: 9344 19.33 - 38.65: 1040 38.65 - 57.98: 288 57.98 - 77.30: 64 77.30 - 96.63: 18 Dihedral angle restraints: 10754 sinusoidal: 4670 harmonic: 6084 Sorted by residual: dihedral pdb=" C3' A H 6 " pdb=" C4' A H 6 " pdb=" O4' A H 6 " pdb=" C1' A H 6 " ideal model delta sinusoidal sigma weight residual 20.00 -7.86 27.86 1 8.00e+00 1.56e-02 1.74e+01 dihedral pdb=" C4' A H 6 " pdb=" O4' A H 6 " pdb=" C1' A H 6 " pdb=" C2' A H 6 " ideal model delta sinusoidal sigma weight residual 3.00 29.45 -26.45 1 8.00e+00 1.56e-02 1.57e+01 dihedral pdb=" CA ASP D 106 " pdb=" C ASP D 106 " pdb=" N ILE D 107 " pdb=" CA ILE D 107 " ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 10751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2083 0.043 - 0.087: 500 0.087 - 0.130: 237 0.130 - 0.173: 31 0.173 - 0.217: 13 Chirality restraints: 2864 Sorted by residual: chirality pdb=" C3' U G 17 " pdb=" C4' U G 17 " pdb=" O3' U G 17 " pdb=" C2' U G 17 " both_signs ideal model delta sigma weight residual False -2.48 -2.69 0.22 2.00e-01 2.50e+01 1.17e+00 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 -2.68 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C3' U G 13 " pdb=" C4' U G 13 " pdb=" O3' U G 13 " pdb=" C2' U G 13 " both_signs ideal model delta sigma weight residual False -2.48 -2.67 0.20 2.00e-01 2.50e+01 9.54e-01 ... (remaining 2861 not shown) Planarity restraints: 2998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 203 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" C PHE B 203 " 0.049 2.00e-02 2.50e+03 pdb=" O PHE B 203 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS B 204 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 204 " 0.038 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO C 205 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 205 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 205 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 226 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.88e+00 pdb=" C LYS E 226 " 0.038 2.00e-02 2.50e+03 pdb=" O LYS E 226 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU E 227 " -0.013 2.00e-02 2.50e+03 ... (remaining 2995 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1408 2.74 - 3.28: 17142 3.28 - 3.82: 30180 3.82 - 4.36: 37190 4.36 - 4.90: 62588 Nonbonded interactions: 148508 Sorted by model distance: nonbonded pdb=" OD1 ASN A 45 " pdb=" OG1 THR A 47 " model vdw 2.204 2.440 nonbonded pdb=" OD2 ASP D 212 " pdb=" OH TYR D 225 " model vdw 2.250 2.440 nonbonded pdb=" OD2 ASP C 212 " pdb=" OH TYR C 225 " model vdw 2.260 2.440 nonbonded pdb=" O HIS A 242 " pdb=" OG SER A 287 " model vdw 2.263 2.440 nonbonded pdb=" O SER F 197 " pdb=" OG SER F 197 " model vdw 2.267 2.440 ... (remaining 148503 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: 2.650 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: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 61.700 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 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 0.072 17953 Z= 0.166 Angle : 0.562 10.139 24577 Z= 0.321 Chirality : 0.048 0.217 2864 Planarity : 0.004 0.057 2998 Dihedral : 17.652 96.628 6830 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.43 % Allowed : 23.39 % Favored : 76.18 % 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: 0.85 (0.24), residues: 528 sheet: 0.35 (0.29), residues: 354 loop : 0.20 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP E 332 HIS 0.003 0.001 HIS E 95 PHE 0.022 0.001 PHE B 203 TYR 0.012 0.001 TYR D 342 ARG 0.004 0.000 ARG C 61 *********************** 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 239 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 231 time to evaluate : 2.872 Fit side-chains revert: symmetry clash REVERT: F 113 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7165 (mp0) REVERT: E 106 ASP cc_start: 0.7281 (m-30) cc_final: 0.6975 (p0) REVERT: B 330 MET cc_start: 0.6707 (tpp) cc_final: 0.6213 (ttm) REVERT: C 218 MET cc_start: 0.7052 (ttt) cc_final: 0.6759 (ttm) outliers start: 8 outliers final: 1 residues processed: 234 average time/residue: 0.3232 time to fit residues: 112.9057 Evaluate side-chains 208 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 207 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 0.0570 chunk 53 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 84 optimal weight: 0.0020 chunk 163 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 188 optimal weight: 0.5980 overall best weight: 0.4306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 HIS E 163 ASN C 11 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17953 Z= 0.161 Angle : 0.508 9.961 24577 Z= 0.264 Chirality : 0.044 0.203 2864 Planarity : 0.004 0.048 2998 Dihedral : 11.207 80.659 2866 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.56 % Allowed : 23.06 % Favored : 75.38 % 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: 0.66 (0.19), residues: 2094 helix: 0.88 (0.24), residues: 534 sheet: 0.63 (0.29), residues: 354 loop : 0.30 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 86 HIS 0.003 0.001 HIS D 337 PHE 0.014 0.001 PHE C 7 TYR 0.011 0.001 TYR D 342 ARG 0.004 0.000 ARG D 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 251 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 222 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 340 THR cc_start: 0.5512 (OUTLIER) cc_final: 0.4868 (p) REVERT: E 106 ASP cc_start: 0.7301 (m-30) cc_final: 0.7071 (p0) REVERT: E 227 LEU cc_start: 0.8435 (mm) cc_final: 0.8184 (mm) REVERT: B 284 GLN cc_start: 0.8036 (tp40) cc_final: 0.7550 (tt0) REVERT: A 252 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8413 (mp) REVERT: C 226 LYS cc_start: 0.8625 (mmtm) cc_final: 0.8031 (ptmm) outliers start: 29 outliers final: 16 residues processed: 248 average time/residue: 0.2908 time to fit residues: 109.7819 Evaluate side-chains 218 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 200 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 144 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 0.0270 chunk 58 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 189 optimal weight: 0.5980 chunk 204 optimal weight: 6.9990 chunk 168 optimal weight: 0.0270 chunk 187 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 163 ASN A 62 ASN A 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17953 Z= 0.164 Angle : 0.496 13.218 24577 Z= 0.254 Chirality : 0.044 0.193 2864 Planarity : 0.003 0.043 2998 Dihedral : 10.584 73.615 2864 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.88 % Allowed : 22.74 % Favored : 75.38 % 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: 0.88 (0.24), residues: 534 sheet: 0.68 (0.30), residues: 330 loop : 0.37 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 86 HIS 0.003 0.001 HIS E 95 PHE 0.013 0.001 PHE E 123 TYR 0.018 0.001 TYR D 278 ARG 0.004 0.000 ARG C 126 *********************** 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 262 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 227 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 135 ARG cc_start: 0.8117 (ttm-80) cc_final: 0.7811 (mtt90) REVERT: E 227 LEU cc_start: 0.8401 (mm) cc_final: 0.8164 (mm) REVERT: A 252 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8417 (mp) REVERT: A 333 CYS cc_start: 0.8643 (m) cc_final: 0.8278 (m) REVERT: C 226 LYS cc_start: 0.8616 (mmtm) cc_final: 0.8063 (ptmm) outliers start: 35 outliers final: 19 residues processed: 254 average time/residue: 0.2845 time to fit residues: 111.2063 Evaluate side-chains 233 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 213 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 288 SER Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain C residue 47 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 189 optimal weight: 0.0070 chunk 201 optimal weight: 0.0570 chunk 99 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 309 GLN E 163 ASN E 244 GLN A 14 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17953 Z= 0.199 Angle : 0.500 11.420 24577 Z= 0.257 Chirality : 0.045 0.404 2864 Planarity : 0.003 0.039 2998 Dihedral : 10.340 74.544 2864 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.04 % Allowed : 22.96 % 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: 0.64 (0.19), residues: 2094 helix: 0.76 (0.24), residues: 540 sheet: 0.51 (0.29), residues: 348 loop : 0.37 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 86 HIS 0.003 0.001 HIS D 337 PHE 0.023 0.001 PHE D 258 TYR 0.016 0.001 TYR D 278 ARG 0.005 0.000 ARG D 90 *********************** 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 252 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 214 time to evaluate : 1.930 Fit side-chains revert: symmetry clash REVERT: D 261 SER cc_start: 0.8366 (OUTLIER) cc_final: 0.8137 (p) REVERT: E 135 ARG cc_start: 0.8191 (ttm-80) cc_final: 0.7946 (mtt90) REVERT: B 218 MET cc_start: 0.7152 (ttt) cc_final: 0.6877 (ttt) REVERT: B 257 ARG cc_start: 0.7435 (tpp80) cc_final: 0.6347 (tpp80) REVERT: A 252 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8445 (mp) REVERT: A 333 CYS cc_start: 0.8666 (m) cc_final: 0.8315 (m) REVERT: C 167 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8306 (pp) REVERT: C 226 LYS cc_start: 0.8591 (mmtm) cc_final: 0.8059 (ptmm) outliers start: 38 outliers final: 25 residues processed: 244 average time/residue: 0.3099 time to fit residues: 115.1337 Evaluate side-chains 227 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 199 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 288 SER Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 171 optimal weight: 0.0370 chunk 138 optimal weight: 0.2980 chunk 0 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 chunk 50 optimal weight: 0.0370 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17953 Z= 0.134 Angle : 0.474 11.333 24577 Z= 0.243 Chirality : 0.043 0.396 2864 Planarity : 0.003 0.038 2998 Dihedral : 10.111 74.572 2864 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.15 % Allowed : 22.90 % 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: 0.71 (0.19), residues: 2094 helix: 0.83 (0.24), residues: 540 sheet: 0.51 (0.28), residues: 348 loop : 0.42 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 86 HIS 0.003 0.001 HIS D 337 PHE 0.024 0.001 PHE D 258 TYR 0.015 0.001 TYR D 278 ARG 0.003 0.000 ARG C 126 *********************** 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 266 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 226 time to evaluate : 1.886 Fit side-chains revert: symmetry clash REVERT: D 187 GLN cc_start: 0.8080 (mt0) cc_final: 0.7827 (mt0) REVERT: D 261 SER cc_start: 0.8273 (OUTLIER) cc_final: 0.8031 (p) REVERT: E 135 ARG cc_start: 0.8157 (ttm-80) cc_final: 0.7932 (mtt90) REVERT: B 132 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7076 (t70) REVERT: B 202 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7203 (tp30) REVERT: B 218 MET cc_start: 0.7127 (ttt) cc_final: 0.6886 (ttt) REVERT: B 284 GLN cc_start: 0.7579 (tp40) cc_final: 0.7157 (tt0) REVERT: A 333 CYS cc_start: 0.8634 (m) cc_final: 0.8304 (m) REVERT: C 226 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8037 (ptmm) REVERT: C 280 ILE cc_start: 0.8584 (mt) cc_final: 0.8357 (mt) outliers start: 40 outliers final: 23 residues processed: 258 average time/residue: 0.2817 time to fit residues: 110.9525 Evaluate side-chains 236 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 210 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 288 SER Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain A residue 63 ILE 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 318 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 148 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 1.9990 chunk 181 optimal weight: 0.0870 chunk 39 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 201 optimal weight: 2.9990 chunk 167 optimal weight: 0.0980 chunk 93 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 105 optimal weight: 0.0170 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN E 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17953 Z= 0.129 Angle : 0.479 11.437 24577 Z= 0.243 Chirality : 0.043 0.408 2864 Planarity : 0.003 0.050 2998 Dihedral : 9.944 73.876 2864 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.61 % Allowed : 23.76 % 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: 0.80 (0.19), residues: 2094 helix: 0.89 (0.24), residues: 540 sheet: 0.66 (0.28), residues: 342 loop : 0.47 (0.19), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 86 HIS 0.003 0.001 HIS D 337 PHE 0.023 0.001 PHE D 258 TYR 0.013 0.001 TYR D 278 ARG 0.008 0.000 ARG B 257 *********************** 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 259 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 229 time to evaluate : 1.765 Fit side-chains revert: symmetry clash REVERT: D 182 VAL cc_start: 0.8971 (t) cc_final: 0.8658 (m) REVERT: D 187 GLN cc_start: 0.7996 (mt0) cc_final: 0.7661 (mt0) REVERT: E 135 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7949 (mtt90) REVERT: B 132 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7053 (t70) REVERT: B 202 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7156 (tp30) REVERT: B 218 MET cc_start: 0.7072 (ttt) cc_final: 0.6865 (ttt) REVERT: B 284 GLN cc_start: 0.7512 (tp40) cc_final: 0.7100 (tt0) REVERT: A 187 GLN cc_start: 0.8488 (mt0) cc_final: 0.8268 (mt0) REVERT: A 333 CYS cc_start: 0.8653 (m) cc_final: 0.8317 (m) REVERT: C 226 LYS cc_start: 0.8475 (mmtm) cc_final: 0.8039 (ptmm) REVERT: C 280 ILE cc_start: 0.8591 (mt) cc_final: 0.8387 (mt) outliers start: 30 outliers final: 22 residues processed: 252 average time/residue: 0.2789 time to fit residues: 106.8507 Evaluate side-chains 234 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 210 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 288 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 47 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 112 optimal weight: 0.0970 chunk 200 optimal weight: 1.9990 chunk 125 optimal weight: 0.0570 chunk 122 optimal weight: 0.3980 chunk 92 optimal weight: 0.0670 overall best weight: 0.3034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17953 Z= 0.131 Angle : 0.482 11.250 24577 Z= 0.243 Chirality : 0.044 0.413 2864 Planarity : 0.003 0.035 2998 Dihedral : 9.852 73.440 2864 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.67 % Allowed : 23.82 % 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: 0.80 (0.19), residues: 2094 helix: 0.87 (0.24), residues: 540 sheet: 0.75 (0.28), residues: 354 loop : 0.44 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 332 HIS 0.004 0.001 HIS A 249 PHE 0.025 0.001 PHE D 258 TYR 0.014 0.001 TYR D 278 ARG 0.005 0.000 ARG B 257 *********************** 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 252 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 221 time to evaluate : 1.716 Fit side-chains revert: symmetry clash REVERT: F 295 ILE cc_start: 0.8093 (pt) cc_final: 0.7785 (mp) REVERT: D 182 VAL cc_start: 0.8960 (t) cc_final: 0.8550 (m) REVERT: D 187 GLN cc_start: 0.7980 (mt0) cc_final: 0.7696 (mt0) REVERT: D 264 GLU cc_start: 0.7683 (mp0) cc_final: 0.7249 (tt0) REVERT: E 135 ARG cc_start: 0.8141 (ttm-80) cc_final: 0.7887 (mtt90) REVERT: B 132 ASP cc_start: 0.7484 (OUTLIER) cc_final: 0.7045 (t70) REVERT: B 202 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7145 (tp30) REVERT: B 218 MET cc_start: 0.7059 (ttt) cc_final: 0.6847 (ttt) REVERT: B 284 GLN cc_start: 0.7449 (tp40) cc_final: 0.7063 (tt0) REVERT: A 187 GLN cc_start: 0.8463 (mt0) cc_final: 0.8232 (mt0) REVERT: A 333 CYS cc_start: 0.8607 (m) cc_final: 0.8331 (m) REVERT: C 167 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8215 (pp) REVERT: C 226 LYS cc_start: 0.8513 (mmtm) cc_final: 0.8120 (ptmm) REVERT: C 330 MET cc_start: 0.6981 (mmm) cc_final: 0.6612 (mmm) outliers start: 31 outliers final: 23 residues processed: 243 average time/residue: 0.2764 time to fit residues: 102.6717 Evaluate side-chains 238 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 212 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 288 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain A residue 63 ILE 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 318 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 167 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 157 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17953 Z= 0.236 Angle : 0.520 11.175 24577 Z= 0.263 Chirality : 0.045 0.428 2864 Planarity : 0.003 0.036 2998 Dihedral : 9.937 73.881 2864 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.83 % Allowed : 23.76 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.19), residues: 2094 helix: 0.75 (0.24), residues: 540 sheet: 0.47 (0.29), residues: 342 loop : 0.35 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 332 HIS 0.003 0.001 HIS E 95 PHE 0.024 0.002 PHE D 258 TYR 0.015 0.001 TYR D 278 ARG 0.004 0.000 ARG D 90 *********************** 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 239 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 205 time to evaluate : 1.852 Fit side-chains revert: symmetry clash REVERT: D 187 GLN cc_start: 0.8069 (mt0) cc_final: 0.7855 (mt0) REVERT: D 264 GLU cc_start: 0.7761 (mp0) cc_final: 0.7295 (tt0) REVERT: E 106 ASP cc_start: 0.7930 (m-30) cc_final: 0.7630 (m-30) REVERT: E 109 LYS cc_start: 0.8651 (mmpt) cc_final: 0.8409 (mmtt) REVERT: B 202 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7193 (tp30) REVERT: B 257 ARG cc_start: 0.7535 (tpp-160) cc_final: 0.6845 (tpp80) REVERT: B 284 GLN cc_start: 0.7584 (tp40) cc_final: 0.7175 (tt0) REVERT: A 333 CYS cc_start: 0.8651 (m) cc_final: 0.8301 (m) REVERT: A 345 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6910 (tp) REVERT: C 167 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8482 (pp) REVERT: C 226 LYS cc_start: 0.8460 (mmtm) cc_final: 0.8081 (ptmm) REVERT: C 330 MET cc_start: 0.7171 (mmm) cc_final: 0.6727 (mmm) outliers start: 34 outliers final: 21 residues processed: 231 average time/residue: 0.3229 time to fit residues: 113.6898 Evaluate side-chains 221 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 197 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 288 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain A residue 63 ILE 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 318 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 167 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 182 optimal weight: 0.4980 chunk 192 optimal weight: 2.9990 chunk 175 optimal weight: 0.3980 chunk 186 optimal weight: 2.9990 chunk 112 optimal weight: 0.0000 chunk 81 optimal weight: 0.0870 chunk 146 optimal weight: 0.1980 chunk 57 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 176 optimal weight: 0.7980 chunk 122 optimal weight: 0.0970 overall best weight: 0.1560 ------------------------------------------------------------------------------- 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: 0.7633 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17953 Z= 0.118 Angle : 0.485 11.428 24577 Z= 0.244 Chirality : 0.043 0.429 2864 Planarity : 0.003 0.034 2998 Dihedral : 9.797 73.461 2864 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.29 % Allowed : 24.19 % 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: 0.80 (0.19), residues: 2094 helix: 0.87 (0.24), residues: 540 sheet: 0.72 (0.28), residues: 354 loop : 0.45 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 332 HIS 0.003 0.001 HIS D 337 PHE 0.026 0.001 PHE D 258 TYR 0.011 0.001 TYR D 278 ARG 0.008 0.000 ARG E 135 *********************** 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 246 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 222 time to evaluate : 1.827 Fit side-chains revert: symmetry clash REVERT: F 302 PHE cc_start: 0.7640 (t80) cc_final: 0.6750 (t80) REVERT: D 182 VAL cc_start: 0.8909 (t) cc_final: 0.8544 (m) REVERT: D 187 GLN cc_start: 0.8010 (mt0) cc_final: 0.7687 (mt0) REVERT: D 264 GLU cc_start: 0.7481 (mp0) cc_final: 0.7260 (tt0) REVERT: B 132 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7040 (t70) REVERT: B 202 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7132 (tp30) REVERT: B 257 ARG cc_start: 0.7441 (tpp-160) cc_final: 0.6804 (tpp80) REVERT: B 277 ASN cc_start: 0.8247 (m-40) cc_final: 0.8045 (m-40) REVERT: B 284 GLN cc_start: 0.7387 (tp40) cc_final: 0.7048 (tt0) REVERT: B 330 MET cc_start: 0.6462 (tpp) cc_final: 0.6259 (ttm) REVERT: A 187 GLN cc_start: 0.8356 (mt0) cc_final: 0.8067 (mt0) REVERT: A 333 CYS cc_start: 0.8610 (m) cc_final: 0.8365 (m) REVERT: A 345 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6835 (tp) REVERT: C 226 LYS cc_start: 0.8433 (mmtm) cc_final: 0.8082 (ptmm) REVERT: C 330 MET cc_start: 0.6883 (mmm) cc_final: 0.6603 (mmm) outliers start: 24 outliers final: 21 residues processed: 240 average time/residue: 0.2835 time to fit residues: 103.6627 Evaluate side-chains 233 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 209 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 288 SER Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 148 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 0.0370 chunk 120 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 190 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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: 0.7695 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17953 Z= 0.204 Angle : 0.509 11.049 24577 Z= 0.257 Chirality : 0.045 0.439 2864 Planarity : 0.003 0.034 2998 Dihedral : 9.830 73.459 2864 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.29 % Allowed : 24.19 % 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: 0.64 (0.19), residues: 2094 helix: 0.81 (0.24), residues: 540 sheet: 0.50 (0.29), residues: 342 loop : 0.35 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 332 HIS 0.003 0.001 HIS E 95 PHE 0.027 0.001 PHE D 258 TYR 0.014 0.001 TYR D 278 ARG 0.007 0.000 ARG E 135 ********************** 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 224 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 200 time to evaluate : 1.886 Fit side-chains revert: symmetry clash REVERT: D 182 VAL cc_start: 0.8963 (t) cc_final: 0.8595 (m) REVERT: D 187 GLN cc_start: 0.8038 (mt0) cc_final: 0.7549 (mt0) REVERT: D 264 GLU cc_start: 0.7595 (mp0) cc_final: 0.7289 (tt0) REVERT: B 202 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7168 (tp30) REVERT: B 257 ARG cc_start: 0.7444 (tpp-160) cc_final: 0.6764 (tpp80) REVERT: B 284 GLN cc_start: 0.7427 (tp40) cc_final: 0.7061 (tt0) REVERT: B 330 MET cc_start: 0.6503 (tpp) cc_final: 0.6282 (ttm) REVERT: A 333 CYS cc_start: 0.8638 (m) cc_final: 0.8315 (m) REVERT: A 345 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6913 (tp) REVERT: C 226 LYS cc_start: 0.8427 (mmtm) cc_final: 0.8092 (ptmm) REVERT: C 330 MET cc_start: 0.7035 (mmm) cc_final: 0.6660 (mmm) outliers start: 24 outliers final: 20 residues processed: 219 average time/residue: 0.2972 time to fit residues: 99.1412 Evaluate side-chains 217 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 195 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 288 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 148 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 152 optimal weight: 0.0980 chunk 24 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 165 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.164307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.122244 restraints weight = 134834.838| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 7.26 r_work: 0.2864 rms_B_bonded: 6.58 restraints_weight: 2.0000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17953 Z= 0.193 Angle : 0.506 11.335 24577 Z= 0.255 Chirality : 0.044 0.436 2864 Planarity : 0.003 0.035 2998 Dihedral : 9.859 73.462 2864 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.29 % Allowed : 24.09 % 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: 0.59 (0.19), residues: 2094 helix: 0.75 (0.24), residues: 540 sheet: 0.59 (0.29), residues: 354 loop : 0.28 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 332 HIS 0.003 0.001 HIS E 95 PHE 0.026 0.001 PHE D 258 TYR 0.014 0.001 TYR D 278 ARG 0.007 0.000 ARG E 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3781.38 seconds wall clock time: 68 minutes 22.17 seconds (4102.17 seconds total)