Starting phenix.real_space_refine on Sun Feb 18 00:35:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzh_22531/02_2024/7jzh_22531.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzh_22531/02_2024/7jzh_22531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzh_22531/02_2024/7jzh_22531.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzh_22531/02_2024/7jzh_22531.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzh_22531/02_2024/7jzh_22531.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzh_22531/02_2024/7jzh_22531.pdb" } resolution = 3.59 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 ------------------------------------------------------------------------------- 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= 0.166 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: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 12948 2.51 5 N 3456 2.21 5 O 3786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 12": "OE1" <-> "OE2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 36": "OE1" <-> "OE2" Residue "A GLU 49": "OE1" <-> "OE2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A ARG 398": "NH1" <-> "NH2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "B GLU 373": "OE1" <-> "OE2" Residue "B ARG 398": "NH1" <-> "NH2" Residue "B GLU 414": "OE1" <-> "OE2" Residue "B GLU 439": "OE1" <-> "OE2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C GLU 36": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "C GLU 200": "OE1" <-> "OE2" Residue "C ARG 266": "NH1" <-> "NH2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C GLU 293": "OE1" <-> "OE2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C GLU 337": "OE1" <-> "OE2" Residue "C GLU 364": "OE1" <-> "OE2" Residue "C GLU 397": "OE1" <-> "OE2" Residue "C ARG 398": "NH1" <-> "NH2" Residue "C GLU 435": "OE1" <-> "OE2" Residue "C TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 36": "OE1" <-> "OE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D GLU 196": "OE1" <-> "OE2" Residue "D ARG 266": "NH1" <-> "NH2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "D GLU 293": "OE1" <-> "OE2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "D GLU 364": "OE1" <-> "OE2" Residue "D GLU 373": "OE1" <-> "OE2" Residue "D TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "D ARG 398": "NH1" <-> "NH2" Residue "D TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 450": "OD1" <-> "OD2" Residue "E GLU 36": "OE1" <-> "OE2" Residue "E GLU 49": "OE1" <-> "OE2" Residue "E GLU 70": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E GLU 176": "OE1" <-> "OE2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "E GLU 218": "OE1" <-> "OE2" Residue "E ARG 266": "NH1" <-> "NH2" Residue "E GLU 292": "OE1" <-> "OE2" Residue "E ARG 336": "NH1" <-> "NH2" Residue "E GLU 337": "OE1" <-> "OE2" Residue "E GLU 364": "OE1" <-> "OE2" Residue "E ARG 398": "NH1" <-> "NH2" Residue "E GLU 430": "OE1" <-> "OE2" Residue "F GLU 12": "OE1" <-> "OE2" Residue "F GLU 28": "OE1" <-> "OE2" Residue "F GLU 36": "OE1" <-> "OE2" Residue "F GLU 70": "OE1" <-> "OE2" Residue "F ASP 86": "OD1" <-> "OD2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "F GLU 200": "OE1" <-> "OE2" Residue "F ARG 266": "NH1" <-> "NH2" Residue "F ARG 336": "NH1" <-> "NH2" Residue "F GLU 337": "OE1" <-> "OE2" Residue "F GLU 364": "OE1" <-> "OE2" Residue "F ARG 398": "NH1" <-> "NH2" Residue "F GLU 430": "OE1" <-> "OE2" Residue "F GLU 435": "OE1" <-> "OE2" Residue "F GLU 439": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20328 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3388 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3388 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3388 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 3388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3388 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 3388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3388 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 3388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3388 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 10.45, per 1000 atoms: 0.51 Number of scatterers: 20328 At special positions: 0 Unit cell: (138.24, 139.32, 93.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 138 16.00 O 3786 8.00 N 3456 7.00 C 12948 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: 7.91 Conformation dependent library (CDL) restraints added in 3.5 seconds 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4740 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 12 sheets defined 47.1% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 5 through 14 Processing helix chain 'A' and resid 38 through 54 removed outlier: 3.803A pdb=" N GLU A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 79 Processing helix chain 'A' and resid 90 through 108 removed outlier: 4.027A pdb=" N ALA A 94 " --> pdb=" O TYR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 149 Processing helix chain 'A' and resid 163 through 173 removed outlier: 3.590A pdb=" N HIS A 167 " --> pdb=" O GLN A 163 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE A 169 " --> pdb=" O CYS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 removed outlier: 3.874A pdb=" N ILE A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 234 removed outlier: 4.334A pdb=" N LEU A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A 225 " --> pdb=" O GLN A 221 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 249 removed outlier: 3.515A pdb=" N PHE A 249 " --> pdb=" O SER A 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 246 through 249' Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 322 through 359 removed outlier: 3.507A pdb=" N ALA A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ARG A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N GLU A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 401 removed outlier: 3.785A pdb=" N LEU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU A 397 " --> pdb=" O TYR A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 451 Processing helix chain 'B' and resid 6 through 14 Processing helix chain 'B' and resid 38 through 54 removed outlier: 3.775A pdb=" N GLU B 49 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 69 through 79 Processing helix chain 'B' and resid 90 through 108 removed outlier: 4.094A pdb=" N ALA B 94 " --> pdb=" O TYR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 149 Processing helix chain 'B' and resid 166 through 173 Processing helix chain 'B' and resid 190 through 197 removed outlier: 3.940A pdb=" N ILE B 195 " --> pdb=" O PRO B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 234 removed outlier: 3.698A pdb=" N ASP B 225 " --> pdb=" O GLN B 221 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA B 226 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 249 Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 322 through 361 removed outlier: 7.546A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLU B 337 " --> pdb=" O ARG B 333 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 361 " --> pdb=" O ILE B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 401 removed outlier: 3.782A pdb=" N LEU B 395 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU B 397 " --> pdb=" O TYR B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 451 Processing helix chain 'C' and resid 6 through 14 Processing helix chain 'C' and resid 38 through 54 removed outlier: 3.885A pdb=" N GLU C 49 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 69 through 79 Processing helix chain 'C' and resid 90 through 108 removed outlier: 4.044A pdb=" N ALA C 94 " --> pdb=" O TYR C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 149 removed outlier: 3.660A pdb=" N ALA C 129 " --> pdb=" O GLY C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 173 Processing helix chain 'C' and resid 190 through 197 removed outlier: 4.032A pdb=" N ILE C 195 " --> pdb=" O PRO C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 234 removed outlier: 4.337A pdb=" N LEU C 223 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP C 225 " --> pdb=" O GLN C 221 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 249 Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 322 through 334 Processing helix chain 'C' and resid 334 through 361 Processing helix chain 'C' and resid 391 through 401 removed outlier: 3.591A pdb=" N LEU C 395 " --> pdb=" O THR C 391 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU C 397 " --> pdb=" O TYR C 393 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG C 398 " --> pdb=" O ASP C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 451 Processing helix chain 'D' and resid 6 through 14 Processing helix chain 'D' and resid 38 through 54 removed outlier: 3.905A pdb=" N GLU D 49 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 69 through 79 Processing helix chain 'D' and resid 90 through 108 removed outlier: 4.024A pdb=" N ALA D 94 " --> pdb=" O TYR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 149 removed outlier: 3.636A pdb=" N ALA D 129 " --> pdb=" O GLY D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 173 Processing helix chain 'D' and resid 190 through 197 removed outlier: 3.991A pdb=" N ILE D 195 " --> pdb=" O PRO D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 234 removed outlier: 4.338A pdb=" N LEU D 223 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA D 226 " --> pdb=" O PRO D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 249 Processing helix chain 'D' and resid 250 through 255 Processing helix chain 'D' and resid 322 through 359 removed outlier: 7.336A pdb=" N ARG D 336 " --> pdb=" O LEU D 332 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N GLU D 337 " --> pdb=" O ARG D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 401 removed outlier: 4.012A pdb=" N GLU D 397 " --> pdb=" O TYR D 393 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG D 398 " --> pdb=" O ASP D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 451 Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 38 through 54 removed outlier: 3.978A pdb=" N GLU E 49 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 59 Processing helix chain 'E' and resid 69 through 80 Processing helix chain 'E' and resid 90 through 108 removed outlier: 4.034A pdb=" N ALA E 94 " --> pdb=" O TYR E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 149 Processing helix chain 'E' and resid 163 through 173 removed outlier: 3.655A pdb=" N HIS E 167 " --> pdb=" O GLN E 163 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N PHE E 169 " --> pdb=" O CYS E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 197 removed outlier: 3.910A pdb=" N ILE E 195 " --> pdb=" O PRO E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 234 removed outlier: 3.539A pdb=" N ASP E 225 " --> pdb=" O GLN E 221 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA E 226 " --> pdb=" O PRO E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 249 Processing helix chain 'E' and resid 250 through 255 Processing helix chain 'E' and resid 322 through 334 Processing helix chain 'E' and resid 334 through 361 removed outlier: 3.637A pdb=" N GLY E 361 " --> pdb=" O ILE E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 401 removed outlier: 3.899A pdb=" N GLU E 397 " --> pdb=" O TYR E 393 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG E 398 " --> pdb=" O ASP E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 451 Processing helix chain 'F' and resid 6 through 14 Processing helix chain 'F' and resid 38 through 54 removed outlier: 4.210A pdb=" N GLU F 49 " --> pdb=" O ILE F 45 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU F 50 " --> pdb=" O ILE F 46 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 69 through 79 Processing helix chain 'F' and resid 90 through 108 removed outlier: 4.044A pdb=" N ALA F 94 " --> pdb=" O TYR F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 149 Processing helix chain 'F' and resid 163 through 173 removed outlier: 4.108A pdb=" N PHE F 169 " --> pdb=" O CYS F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 197 removed outlier: 3.996A pdb=" N ILE F 195 " --> pdb=" O PRO F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 234 removed outlier: 3.569A pdb=" N ASP F 225 " --> pdb=" O GLN F 221 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA F 226 " --> pdb=" O PRO F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 249 removed outlier: 3.517A pdb=" N PHE F 249 " --> pdb=" O SER F 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 246 through 249' Processing helix chain 'F' and resid 250 through 255 Processing helix chain 'F' and resid 322 through 334 Processing helix chain 'F' and resid 334 through 361 removed outlier: 3.752A pdb=" N GLY F 361 " --> pdb=" O ILE F 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 401 removed outlier: 3.607A pdb=" N LEU F 395 " --> pdb=" O THR F 391 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU F 397 " --> pdb=" O TYR F 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 451 Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 123 removed outlier: 6.557A pdb=" N MET A 240 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER A 269 " --> pdb=" O MET A 240 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 363 through 367 removed outlier: 5.283A pdb=" N PHE A 365 " --> pdb=" O LYS A 381 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS A 381 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 382 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL A 419 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 121 through 123 removed outlier: 6.513A pdb=" N MET B 240 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER B 269 " --> pdb=" O MET B 240 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 363 through 367 removed outlier: 5.329A pdb=" N PHE B 365 " --> pdb=" O LYS B 381 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LYS B 381 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU B 382 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL B 419 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 120 through 123 removed outlier: 7.021A pdb=" N MET C 240 " --> pdb=" O SER C 269 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N SER C 271 " --> pdb=" O MET C 240 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE C 242 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N SER C 273 " --> pdb=" O ILE C 242 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 363 through 367 removed outlier: 5.117A pdb=" N PHE C 365 " --> pdb=" O LYS C 381 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS C 381 " --> pdb=" O PHE C 365 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU C 382 " --> pdb=" O VAL C 419 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL C 419 " --> pdb=" O LEU C 382 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 120 through 123 removed outlier: 6.993A pdb=" N MET D 240 " --> pdb=" O SER D 269 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N SER D 271 " --> pdb=" O MET D 240 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE D 242 " --> pdb=" O SER D 271 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N SER D 273 " --> pdb=" O ILE D 242 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 363 through 367 removed outlier: 5.104A pdb=" N PHE D 365 " --> pdb=" O LYS D 381 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS D 381 " --> pdb=" O PHE D 365 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU D 382 " --> pdb=" O VAL D 419 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL D 419 " --> pdb=" O LEU D 382 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 120 through 123 removed outlier: 7.036A pdb=" N MET E 240 " --> pdb=" O SER E 269 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N SER E 271 " --> pdb=" O MET E 240 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE E 242 " --> pdb=" O SER E 271 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N SER E 273 " --> pdb=" O ILE E 242 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 363 through 367 removed outlier: 5.370A pdb=" N PHE E 365 " --> pdb=" O LYS E 381 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS E 381 " --> pdb=" O PHE E 365 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU E 382 " --> pdb=" O VAL E 419 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL E 419 " --> pdb=" O LEU E 382 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 120 through 123 removed outlier: 7.045A pdb=" N MET F 240 " --> pdb=" O SER F 269 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N SER F 271 " --> pdb=" O MET F 240 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE F 242 " --> pdb=" O SER F 271 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N SER F 273 " --> pdb=" O ILE F 242 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 363 through 367 removed outlier: 5.351A pdb=" N PHE F 365 " --> pdb=" O LYS F 381 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS F 381 " --> pdb=" O PHE F 365 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU F 382 " --> pdb=" O VAL F 419 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL F 419 " --> pdb=" O LEU F 382 " (cutoff:3.500A) 888 hydrogen bonds defined for protein. 2583 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.46 Time building geometry restraints manager: 8.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5951 1.33 - 1.45: 3680 1.45 - 1.58: 10979 1.58 - 1.70: 0 1.70 - 1.82: 216 Bond restraints: 20826 Sorted by residual: bond pdb=" CA ASP B 261 " pdb=" C ASP B 261 " ideal model delta sigma weight residual 1.523 1.560 -0.037 1.34e-02 5.57e+03 7.50e+00 bond pdb=" CA TRP D 260 " pdb=" CB TRP D 260 " ideal model delta sigma weight residual 1.536 1.498 0.039 1.46e-02 4.69e+03 7.01e+00 bond pdb=" N LYS F 276 " pdb=" CA LYS F 276 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.20e-02 6.94e+03 6.54e+00 bond pdb=" CA TRP C 260 " pdb=" CB TRP C 260 " ideal model delta sigma weight residual 1.536 1.497 0.039 1.58e-02 4.01e+03 6.08e+00 bond pdb=" CG1 ILE B 258 " pdb=" CD1 ILE B 258 " ideal model delta sigma weight residual 1.513 1.432 0.081 3.90e-02 6.57e+02 4.31e+00 ... (remaining 20821 not shown) Histogram of bond angle deviations from ideal: 97.17 - 104.56: 405 104.56 - 111.95: 9587 111.95 - 119.35: 7272 119.35 - 126.74: 10551 126.74 - 134.14: 403 Bond angle restraints: 28218 Sorted by residual: angle pdb=" N VAL D 259 " pdb=" CA VAL D 259 " pdb=" C VAL D 259 " ideal model delta sigma weight residual 107.73 121.17 -13.44 1.56e+00 4.11e-01 7.42e+01 angle pdb=" N VAL C 259 " pdb=" CA VAL C 259 " pdb=" C VAL C 259 " ideal model delta sigma weight residual 106.85 118.27 -11.42 1.42e+00 4.96e-01 6.47e+01 angle pdb=" N GLY F 215 " pdb=" CA GLY F 215 " pdb=" C GLY F 215 " ideal model delta sigma weight residual 112.77 122.95 -10.18 1.28e+00 6.10e-01 6.32e+01 angle pdb=" C LEU A 295 " pdb=" N PRO A 296 " pdb=" CA PRO A 296 " ideal model delta sigma weight residual 120.21 127.77 -7.56 9.60e-01 1.09e+00 6.21e+01 angle pdb=" N GLY B 215 " pdb=" CA GLY B 215 " pdb=" C GLY B 215 " ideal model delta sigma weight residual 112.77 122.79 -10.02 1.28e+00 6.10e-01 6.12e+01 ... (remaining 28213 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 10156 18.10 - 36.21: 1527 36.21 - 54.31: 519 54.31 - 72.42: 144 72.42 - 90.52: 50 Dihedral angle restraints: 12396 sinusoidal: 5022 harmonic: 7374 Sorted by residual: dihedral pdb=" CA GLU D 218 " pdb=" C GLU D 218 " pdb=" N PHE D 219 " pdb=" CA PHE D 219 " ideal model delta harmonic sigma weight residual -180.00 -151.63 -28.37 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" C TYR D 213 " pdb=" N TYR D 213 " pdb=" CA TYR D 213 " pdb=" CB TYR D 213 " ideal model delta harmonic sigma weight residual -122.60 -136.16 13.56 0 2.50e+00 1.60e-01 2.94e+01 dihedral pdb=" N TYR D 213 " pdb=" C TYR D 213 " pdb=" CA TYR D 213 " pdb=" CB TYR D 213 " ideal model delta harmonic sigma weight residual 122.80 135.80 -13.00 0 2.50e+00 1.60e-01 2.70e+01 ... (remaining 12393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 2882 0.119 - 0.238: 91 0.238 - 0.357: 5 0.357 - 0.476: 0 0.476 - 0.596: 4 Chirality restraints: 2982 Sorted by residual: chirality pdb=" CA TYR D 213 " pdb=" N TYR D 213 " pdb=" C TYR D 213 " pdb=" CB TYR D 213 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.87e+00 chirality pdb=" CA TYR B 213 " pdb=" N TYR B 213 " pdb=" C TYR B 213 " pdb=" CB TYR B 213 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.79e+00 chirality pdb=" CA TYR C 213 " pdb=" N TYR C 213 " pdb=" C TYR C 213 " pdb=" CB TYR C 213 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.78e+00 ... (remaining 2979 not shown) Planarity restraints: 3690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP C 141 " 0.028 2.00e-02 2.50e+03 5.44e-02 2.95e+01 pdb=" C TRP C 141 " -0.094 2.00e-02 2.50e+03 pdb=" O TRP C 141 " 0.035 2.00e-02 2.50e+03 pdb=" N ARG C 142 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 210 " 0.017 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C GLY B 210 " -0.061 2.00e-02 2.50e+03 pdb=" O GLY B 210 " 0.023 2.00e-02 2.50e+03 pdb=" N VAL B 211 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 219 " 0.043 5.00e-02 4.00e+02 6.56e-02 6.88e+00 pdb=" N PRO C 220 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 220 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 220 " 0.037 5.00e-02 4.00e+02 ... (remaining 3687 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 450 2.66 - 3.22: 19435 3.22 - 3.78: 30811 3.78 - 4.34: 40596 4.34 - 4.90: 66344 Nonbonded interactions: 157636 Sorted by model distance: nonbonded pdb=" N GLU B 89 " pdb=" OE1 GLU B 89 " model vdw 2.095 2.520 nonbonded pdb=" OD1 ASP E 86 " pdb=" N LYS E 87 " model vdw 2.162 2.520 nonbonded pdb=" OD1 ASP A 86 " pdb=" N LYS A 87 " model vdw 2.175 2.520 nonbonded pdb=" N GLN B 297 " pdb=" OE1 GLN B 297 " model vdw 2.179 2.520 nonbonded pdb=" O GLN E 163 " pdb=" ND1 HIS E 167 " model vdw 2.202 2.520 ... (remaining 157631 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 1.750 Check model and map are aligned: 0.410 Set scattering table: 0.200 Process input model: 51.360 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 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 : 0.006 0.081 20826 Z= 0.423 Angle : 0.956 13.438 28218 Z= 0.565 Chirality : 0.056 0.596 2982 Planarity : 0.006 0.066 3690 Dihedral : 20.562 90.525 7656 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.67 % Favored : 91.29 % Rotamer: Outliers : 16.34 % Allowed : 33.24 % Favored : 50.42 % Cbeta Deviations : 0.17 % 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: -3.42 (0.14), residues: 2526 helix: -2.06 (0.13), residues: 1110 sheet: -1.10 (0.33), residues: 240 loop : -2.71 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP F 67 HIS 0.011 0.001 HIS C 167 PHE 0.028 0.002 PHE E 230 TYR 0.012 0.002 TYR B 328 ARG 0.015 0.001 ARG A 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 348 poor density : 483 time to evaluate : 2.427 Fit side-chains REVERT: A 45 ILE cc_start: 0.8944 (mt) cc_final: 0.8671 (mt) REVERT: A 49 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7505 (mm-30) REVERT: A 81 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.7791 (m110) REVERT: A 145 MET cc_start: 0.6634 (tpp) cc_final: 0.6045 (mmt) REVERT: A 150 LYS cc_start: 0.8980 (mppt) cc_final: 0.8302 (ttpt) REVERT: A 297 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7149 (mm-40) REVERT: A 336 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7698 (ttm170) REVERT: A 398 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7836 (mmp-170) REVERT: B 37 MET cc_start: 0.7883 (ptp) cc_final: 0.7472 (ptp) REVERT: B 44 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7399 (mm-40) REVERT: B 45 ILE cc_start: 0.8909 (mt) cc_final: 0.8638 (mt) REVERT: B 49 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7442 (mm-30) REVERT: B 84 TRP cc_start: 0.6859 (p-90) cc_final: 0.6555 (p-90) REVERT: B 139 TRP cc_start: 0.6420 (t-100) cc_final: 0.6155 (t-100) REVERT: B 157 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6908 (tp) REVERT: B 201 ASN cc_start: 0.5604 (OUTLIER) cc_final: 0.5402 (t0) REVERT: B 218 GLU cc_start: 0.6184 (tt0) cc_final: 0.5913 (mt-10) REVERT: B 336 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7508 (ttm170) REVERT: B 346 SER cc_start: 0.8684 (t) cc_final: 0.8461 (m) REVERT: C 10 ARG cc_start: 0.5331 (OUTLIER) cc_final: 0.4455 (ptp-170) REVERT: C 57 ARG cc_start: 0.8455 (tpt-90) cc_final: 0.7758 (tpt-90) REVERT: C 63 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7705 (m-80) REVERT: C 84 TRP cc_start: 0.6372 (p-90) cc_final: 0.5838 (p-90) REVERT: C 109 HIS cc_start: 0.6488 (m-70) cc_final: 0.6223 (m170) REVERT: C 131 MET cc_start: 0.4013 (OUTLIER) cc_final: 0.3562 (ttt) REVERT: C 154 LYS cc_start: 0.6398 (OUTLIER) cc_final: 0.6148 (ptmm) REVERT: C 176 GLU cc_start: 0.6266 (OUTLIER) cc_final: 0.5706 (tt0) REVERT: C 218 GLU cc_start: 0.6344 (tt0) cc_final: 0.5679 (mt-10) REVERT: C 236 ILE cc_start: 0.5351 (OUTLIER) cc_final: 0.4754 (mm) REVERT: C 291 ASP cc_start: 0.7504 (p0) cc_final: 0.7269 (p0) REVERT: C 402 ARG cc_start: 0.7302 (mmm-85) cc_final: 0.6964 (mmt180) REVERT: D 28 GLU cc_start: 0.7218 (tp30) cc_final: 0.6874 (tp30) REVERT: D 34 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8638 (mt) REVERT: D 57 ARG cc_start: 0.8485 (tpt-90) cc_final: 0.7377 (tpt-90) REVERT: D 63 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.7795 (m-80) REVERT: D 82 LYS cc_start: 0.7768 (pttm) cc_final: 0.7385 (mtmm) REVERT: D 84 TRP cc_start: 0.6215 (p-90) cc_final: 0.5587 (p-90) REVERT: D 109 HIS cc_start: 0.6459 (m-70) cc_final: 0.6226 (m170) REVERT: D 154 LYS cc_start: 0.6052 (OUTLIER) cc_final: 0.5819 (ptmm) REVERT: D 171 ARG cc_start: 0.4100 (OUTLIER) cc_final: 0.3838 (tpt-90) REVERT: D 236 ILE cc_start: 0.5508 (OUTLIER) cc_final: 0.5142 (mm) REVERT: D 336 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7530 (mmm-85) REVERT: D 459 GLN cc_start: 0.2921 (OUTLIER) cc_final: 0.1456 (pp30) REVERT: E 15 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7850 (t70) REVERT: E 28 GLU cc_start: 0.7418 (tp30) cc_final: 0.7195 (tp30) REVERT: E 44 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7778 (mm-40) REVERT: E 115 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8380 (p0) REVERT: E 124 ILE cc_start: 0.7483 (mm) cc_final: 0.7108 (pt) REVERT: E 141 TRP cc_start: 0.5747 (OUTLIER) cc_final: 0.4801 (t-100) REVERT: E 150 LYS cc_start: 0.9092 (mppt) cc_final: 0.8373 (tttt) REVERT: E 192 LYS cc_start: -0.1269 (OUTLIER) cc_final: -0.1785 (tptt) REVERT: E 373 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7287 (tm-30) REVERT: E 430 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7156 (pm20) REVERT: E 441 TYR cc_start: 0.7623 (OUTLIER) cc_final: 0.7290 (m-80) REVERT: F 31 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7478 (mtm-85) REVERT: F 44 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7802 (mm-40) REVERT: F 117 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.6768 (tm-30) REVERT: F 124 ILE cc_start: 0.7552 (mp) cc_final: 0.7249 (pt) REVERT: F 141 TRP cc_start: 0.5587 (OUTLIER) cc_final: 0.4164 (t-100) REVERT: F 150 LYS cc_start: 0.9076 (mppt) cc_final: 0.8192 (tttt) REVERT: F 381 LYS cc_start: 0.7796 (pttt) cc_final: 0.7345 (pttt) REVERT: F 436 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7264 (mm) REVERT: F 441 TYR cc_start: 0.7672 (OUTLIER) cc_final: 0.7126 (m-80) outliers start: 348 outliers final: 187 residues processed: 762 average time/residue: 0.3332 time to fit residues: 381.6730 Evaluate side-chains 668 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 448 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 344 ASN Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 398 ARG Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 433 PHE Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 141 TRP Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 154 LYS Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 231 GLN Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 344 ASN Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 387 ASP Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain D residue 459 GLN Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 141 TRP Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 402 ARG Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 418 ILE Chi-restraints excluded: chain E residue 430 GLU Chi-restraints excluded: chain E residue 433 PHE Chi-restraints excluded: chain E residue 441 TYR Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 31 ARG Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 117 GLN Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 141 TRP Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 396 SER Chi-restraints excluded: chain F residue 402 ARG Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 430 GLU Chi-restraints excluded: chain F residue 433 PHE Chi-restraints excluded: chain F residue 436 LEU Chi-restraints excluded: chain F residue 441 TYR Chi-restraints excluded: chain F residue 448 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 20.0000 chunk 191 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 197 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 147 optimal weight: 7.9990 chunk 228 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN C 73 HIS C 201 ASN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS E 73 HIS F 73 HIS ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20826 Z= 0.256 Angle : 0.698 9.733 28218 Z= 0.348 Chirality : 0.046 0.258 2982 Planarity : 0.005 0.064 3690 Dihedral : 11.714 75.545 3162 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 10.09 % Allowed : 32.35 % Favored : 57.56 % 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: -1.94 (0.16), residues: 2526 helix: -0.52 (0.15), residues: 1134 sheet: -1.08 (0.33), residues: 246 loop : -2.10 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 84 HIS 0.005 0.001 HIS C 73 PHE 0.034 0.002 PHE B 230 TYR 0.013 0.001 TYR D 447 ARG 0.007 0.001 ARG B 398 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 447 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.7693 (mm-40) cc_final: 0.7395 (mm-40) REVERT: A 49 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7570 (mm-30) REVERT: A 84 TRP cc_start: 0.6542 (p-90) cc_final: 0.6129 (p-90) REVERT: A 139 TRP cc_start: 0.6001 (OUTLIER) cc_final: 0.5348 (m100) REVERT: A 150 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8249 (tttt) REVERT: A 192 LYS cc_start: -0.0474 (OUTLIER) cc_final: -0.1469 (tptt) REVERT: A 239 ASP cc_start: 0.6993 (OUTLIER) cc_final: 0.6740 (m-30) REVERT: A 336 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7508 (mtp85) REVERT: B 37 MET cc_start: 0.7773 (ptp) cc_final: 0.7157 (ptp) REVERT: B 44 GLN cc_start: 0.7761 (mm-40) cc_final: 0.7344 (mm-40) REVERT: B 45 ILE cc_start: 0.8750 (mt) cc_final: 0.7659 (mt) REVERT: B 49 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7551 (mp0) REVERT: B 84 TRP cc_start: 0.6828 (p-90) cc_final: 0.6549 (p-90) REVERT: B 139 TRP cc_start: 0.6343 (t-100) cc_final: 0.6057 (t-100) REVERT: B 216 ASN cc_start: 0.7031 (OUTLIER) cc_final: 0.6773 (p0) REVERT: B 218 GLU cc_start: 0.6063 (tt0) cc_final: 0.5859 (mt-10) REVERT: B 346 SER cc_start: 0.8641 (t) cc_final: 0.8399 (m) REVERT: C 57 ARG cc_start: 0.8316 (tpt-90) cc_final: 0.7682 (tpt-90) REVERT: C 63 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7671 (m-80) REVERT: C 76 MET cc_start: 0.8465 (tmm) cc_final: 0.7995 (tmm) REVERT: C 78 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8881 (mm) REVERT: C 84 TRP cc_start: 0.6478 (p-90) cc_final: 0.6173 (p-90) REVERT: C 176 GLU cc_start: 0.5900 (OUTLIER) cc_final: 0.5444 (tt0) REVERT: C 218 GLU cc_start: 0.6470 (tt0) cc_final: 0.6153 (mt-10) REVERT: C 402 ARG cc_start: 0.7236 (mmm-85) cc_final: 0.6918 (mmt180) REVERT: D 48 ASP cc_start: 0.7138 (OUTLIER) cc_final: 0.6471 (m-30) REVERT: D 63 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7719 (m-80) REVERT: D 84 TRP cc_start: 0.6218 (p-90) cc_final: 0.5662 (p-90) REVERT: D 87 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7561 (pttt) REVERT: D 373 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7604 (tp30) REVERT: E 57 ARG cc_start: 0.8432 (tpt-90) cc_final: 0.8215 (tpp-160) REVERT: E 74 LYS cc_start: 0.8804 (mtmm) cc_final: 0.8436 (mtmm) REVERT: E 131 MET cc_start: 0.5381 (ttp) cc_final: 0.5130 (ttt) REVERT: E 137 MET cc_start: 0.7425 (mmm) cc_final: 0.6705 (mmt) REVERT: E 141 TRP cc_start: 0.5617 (OUTLIER) cc_final: 0.3914 (t-100) REVERT: E 145 MET cc_start: 0.6479 (mmm) cc_final: 0.5856 (mmt) REVERT: E 324 VAL cc_start: 0.8073 (OUTLIER) cc_final: 0.7822 (m) REVERT: E 373 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7226 (tp30) REVERT: E 381 LYS cc_start: 0.7708 (ptpt) cc_final: 0.7479 (ptpt) REVERT: E 392 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7959 (mt) REVERT: E 441 TYR cc_start: 0.7622 (OUTLIER) cc_final: 0.7292 (m-80) REVERT: F 124 ILE cc_start: 0.7288 (mp) cc_final: 0.7030 (pt) REVERT: F 137 MET cc_start: 0.7488 (mmm) cc_final: 0.6496 (mmt) REVERT: F 141 TRP cc_start: 0.5551 (OUTLIER) cc_final: 0.3985 (t-100) REVERT: F 145 MET cc_start: 0.6418 (mmm) cc_final: 0.5595 (mmt) REVERT: F 150 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8115 (tttt) REVERT: F 216 ASN cc_start: 0.6307 (OUTLIER) cc_final: 0.6106 (p0) REVERT: F 373 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7617 (tp30) REVERT: F 381 LYS cc_start: 0.7609 (pttt) cc_final: 0.7278 (pttt) REVERT: F 392 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7756 (mt) REVERT: F 432 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7329 (p0) REVERT: F 441 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.7186 (m-80) outliers start: 215 outliers final: 113 residues processed: 607 average time/residue: 0.3292 time to fit residues: 301.0458 Evaluate side-chains 554 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 416 time to evaluate : 2.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 139 TRP Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 433 PHE Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 141 TRP Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 141 TRP Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 402 ARG Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 430 GLU Chi-restraints excluded: chain E residue 433 PHE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 441 TYR Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 141 TRP Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 396 SER Chi-restraints excluded: chain F residue 402 ARG Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 430 GLU Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 433 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 441 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 40.0000 chunk 71 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 229 optimal weight: 6.9990 chunk 247 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 chunk 227 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 183 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 HIS C 117 GLN C 201 ASN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS D 156 ASN E 73 HIS F 73 HIS ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20826 Z= 0.267 Angle : 0.688 11.979 28218 Z= 0.334 Chirality : 0.044 0.226 2982 Planarity : 0.005 0.055 3690 Dihedral : 9.821 71.471 2942 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 9.81 % Allowed : 32.07 % Favored : 58.12 % 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: -1.33 (0.16), residues: 2526 helix: 0.06 (0.15), residues: 1158 sheet: -0.92 (0.34), residues: 246 loop : -1.87 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 173 HIS 0.007 0.001 HIS C 73 PHE 0.033 0.002 PHE A 230 TYR 0.015 0.001 TYR A 339 ARG 0.009 0.001 ARG B 398 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 429 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8128 (tpp80) cc_final: 0.7909 (tpp80) REVERT: A 37 MET cc_start: 0.7950 (ptp) cc_final: 0.7490 (ptp) REVERT: A 44 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7473 (mm-40) REVERT: A 49 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: A 84 TRP cc_start: 0.6578 (p-90) cc_final: 0.6090 (p-90) REVERT: A 132 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7238 (tt) REVERT: A 137 MET cc_start: 0.7217 (mmp) cc_final: 0.6822 (mmm) REVERT: A 150 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8138 (ttmt) REVERT: A 192 LYS cc_start: -0.0418 (OUTLIER) cc_final: -0.1484 (tptt) REVERT: A 421 MET cc_start: 0.8519 (ttp) cc_final: 0.8278 (ttp) REVERT: B 37 MET cc_start: 0.7785 (ptp) cc_final: 0.7180 (ptp) REVERT: B 44 GLN cc_start: 0.7686 (mm-40) cc_final: 0.7339 (mm-40) REVERT: B 45 ILE cc_start: 0.8710 (mt) cc_final: 0.7722 (mt) REVERT: B 49 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: B 84 TRP cc_start: 0.6895 (p-90) cc_final: 0.6542 (p-90) REVERT: B 139 TRP cc_start: 0.6392 (t-100) cc_final: 0.6115 (t-100) REVERT: B 216 ASN cc_start: 0.7025 (OUTLIER) cc_final: 0.6509 (p0) REVERT: B 346 SER cc_start: 0.8623 (t) cc_final: 0.8391 (m) REVERT: B 421 MET cc_start: 0.8517 (ttp) cc_final: 0.8294 (ttp) REVERT: C 57 ARG cc_start: 0.8296 (tpt-90) cc_final: 0.7287 (tpt-90) REVERT: C 63 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7623 (m-80) REVERT: C 78 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8839 (mm) REVERT: C 84 TRP cc_start: 0.6559 (p-90) cc_final: 0.6118 (p-90) REVERT: C 176 GLU cc_start: 0.5709 (OUTLIER) cc_final: 0.5287 (tt0) REVERT: C 218 GLU cc_start: 0.6549 (tt0) cc_final: 0.6249 (mt-10) REVERT: C 402 ARG cc_start: 0.7203 (mmm-85) cc_final: 0.6899 (mmt180) REVERT: D 84 TRP cc_start: 0.6320 (p-90) cc_final: 0.6030 (p-90) REVERT: D 87 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7576 (pttt) REVERT: D 145 MET cc_start: 0.5431 (mmt) cc_final: 0.5145 (mmm) REVERT: D 373 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7414 (tm-30) REVERT: E 31 ARG cc_start: 0.7943 (mtm-85) cc_final: 0.7614 (mmt90) REVERT: E 57 ARG cc_start: 0.8441 (tpt-90) cc_final: 0.8220 (tpp-160) REVERT: E 76 MET cc_start: 0.8535 (tmt) cc_final: 0.8221 (tmm) REVERT: E 84 TRP cc_start: 0.6893 (p-90) cc_final: 0.6312 (p-90) REVERT: E 115 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.8376 (p0) REVERT: E 135 MET cc_start: 0.6833 (tpt) cc_final: 0.6452 (ttm) REVERT: E 141 TRP cc_start: 0.5489 (OUTLIER) cc_final: 0.3682 (t-100) REVERT: E 145 MET cc_start: 0.6266 (mmm) cc_final: 0.5657 (mmt) REVERT: E 150 LYS cc_start: 0.9063 (mmmt) cc_final: 0.8292 (ttmt) REVERT: E 192 LYS cc_start: -0.1028 (OUTLIER) cc_final: -0.1495 (tptt) REVERT: E 324 VAL cc_start: 0.8089 (OUTLIER) cc_final: 0.7874 (m) REVERT: E 373 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7320 (tp30) REVERT: E 381 LYS cc_start: 0.7702 (ptpt) cc_final: 0.7467 (ptpt) REVERT: E 432 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7033 (p0) REVERT: E 455 GLN cc_start: 0.6422 (OUTLIER) cc_final: 0.5847 (mt0) REVERT: F 137 MET cc_start: 0.7556 (mmm) cc_final: 0.6997 (mmt) REVERT: F 141 TRP cc_start: 0.5536 (OUTLIER) cc_final: 0.3894 (t-100) REVERT: F 145 MET cc_start: 0.6395 (mmm) cc_final: 0.5677 (mmt) REVERT: F 150 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8037 (ttmt) REVERT: F 373 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7108 (mt-10) REVERT: F 381 LYS cc_start: 0.7629 (pttt) cc_final: 0.7291 (pttt) REVERT: F 441 TYR cc_start: 0.7616 (OUTLIER) cc_final: 0.7244 (m-80) outliers start: 209 outliers final: 133 residues processed: 586 average time/residue: 0.3176 time to fit residues: 282.7126 Evaluate side-chains 565 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 412 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 433 PHE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 139 TRP Chi-restraints excluded: chain C residue 141 TRP Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 387 ASP Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 141 TRP Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 402 ARG Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 433 PHE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 455 GLN Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 141 TRP Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 359 LYS Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 402 ARG Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 433 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 441 TYR Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 448 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 6.9990 chunk 172 optimal weight: 20.0000 chunk 118 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 153 optimal weight: 9.9990 chunk 230 optimal weight: 10.0000 chunk 243 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 218 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 HIS ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS E 73 HIS F 73 HIS ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20826 Z= 0.263 Angle : 0.682 11.656 28218 Z= 0.327 Chirality : 0.044 0.232 2982 Planarity : 0.004 0.044 3690 Dihedral : 8.956 70.442 2905 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 9.48 % Allowed : 31.78 % Favored : 58.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.17), residues: 2526 helix: 0.44 (0.15), residues: 1146 sheet: -0.83 (0.34), residues: 246 loop : -1.81 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 141 HIS 0.006 0.001 HIS C 73 PHE 0.032 0.002 PHE A 230 TYR 0.019 0.001 TYR B 172 ARG 0.008 0.000 ARG B 398 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 408 time to evaluate : 2.419 Fit side-chains REVERT: A 30 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7777 (mtmt) REVERT: A 31 ARG cc_start: 0.7946 (tpp80) cc_final: 0.7695 (tpp80) REVERT: A 44 GLN cc_start: 0.7696 (mm-40) cc_final: 0.7356 (mm-40) REVERT: A 45 ILE cc_start: 0.8746 (mt) cc_final: 0.7567 (mt) REVERT: A 49 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: A 75 LEU cc_start: 0.8790 (tp) cc_final: 0.8499 (tp) REVERT: A 84 TRP cc_start: 0.6641 (p-90) cc_final: 0.6321 (p-90) REVERT: A 115 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.8090 (p0) REVERT: A 132 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7238 (tt) REVERT: A 137 MET cc_start: 0.7152 (mmp) cc_final: 0.6729 (mmm) REVERT: A 192 LYS cc_start: -0.0623 (OUTLIER) cc_final: -0.1432 (tptt) REVERT: A 421 MET cc_start: 0.8539 (ttp) cc_final: 0.8323 (ttp) REVERT: B 37 MET cc_start: 0.7773 (ptp) cc_final: 0.7517 (ptp) REVERT: B 44 GLN cc_start: 0.7706 (mm-40) cc_final: 0.7376 (mm-40) REVERT: B 45 ILE cc_start: 0.8731 (mt) cc_final: 0.7839 (mt) REVERT: B 49 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: B 138 LYS cc_start: 0.8214 (ttpp) cc_final: 0.7905 (tmtt) REVERT: B 172 TYR cc_start: 0.3695 (OUTLIER) cc_final: 0.3402 (t80) REVERT: B 216 ASN cc_start: 0.7143 (OUTLIER) cc_final: 0.6154 (p0) REVERT: B 346 SER cc_start: 0.8628 (t) cc_final: 0.8380 (m) REVERT: B 373 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7251 (tm-30) REVERT: B 400 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7282 (ttm-80) REVERT: C 57 ARG cc_start: 0.8301 (tpt-90) cc_final: 0.7314 (tpt-90) REVERT: C 63 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7616 (m-80) REVERT: C 76 MET cc_start: 0.8495 (tmm) cc_final: 0.7943 (tmm) REVERT: C 78 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8776 (mm) REVERT: C 139 TRP cc_start: 0.6467 (OUTLIER) cc_final: 0.5581 (m100) REVERT: C 176 GLU cc_start: 0.5670 (OUTLIER) cc_final: 0.5250 (tt0) REVERT: C 218 GLU cc_start: 0.6520 (tt0) cc_final: 0.6254 (mt-10) REVERT: C 402 ARG cc_start: 0.7429 (mmm-85) cc_final: 0.7133 (mmt180) REVERT: C 459 GLN cc_start: 0.3132 (OUTLIER) cc_final: 0.1808 (pp30) REVERT: D 57 ARG cc_start: 0.8340 (tpt-90) cc_final: 0.7790 (tpt-90) REVERT: D 145 MET cc_start: 0.5248 (mmt) cc_final: 0.4966 (mmm) REVERT: D 168 LYS cc_start: 0.6884 (mmpt) cc_final: 0.6669 (mmpt) REVERT: E 31 ARG cc_start: 0.7577 (mtm-85) cc_final: 0.7374 (mtp85) REVERT: E 57 ARG cc_start: 0.8519 (tpt-90) cc_final: 0.8317 (tpp-160) REVERT: E 76 MET cc_start: 0.8457 (tmt) cc_final: 0.8139 (tmm) REVERT: E 84 TRP cc_start: 0.6927 (p-90) cc_final: 0.6319 (p-90) REVERT: E 135 MET cc_start: 0.7071 (tpt) cc_final: 0.6287 (mtt) REVERT: E 141 TRP cc_start: 0.5363 (OUTLIER) cc_final: 0.3620 (t-100) REVERT: E 145 MET cc_start: 0.6344 (mmm) cc_final: 0.5900 (mmt) REVERT: E 150 LYS cc_start: 0.9051 (mmmt) cc_final: 0.8437 (tmtt) REVERT: E 192 LYS cc_start: -0.1062 (OUTLIER) cc_final: -0.1644 (tptt) REVERT: E 373 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7550 (tp30) REVERT: E 455 GLN cc_start: 0.6419 (OUTLIER) cc_final: 0.5834 (mt0) REVERT: F 141 TRP cc_start: 0.5525 (OUTLIER) cc_final: 0.3950 (t-100) REVERT: F 145 MET cc_start: 0.6423 (mmm) cc_final: 0.5646 (mmt) REVERT: F 150 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8150 (ttmt) REVERT: F 373 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7549 (tp30) REVERT: F 381 LYS cc_start: 0.7609 (pttt) cc_final: 0.7240 (pttt) REVERT: F 441 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.7216 (m-80) outliers start: 202 outliers final: 143 residues processed: 562 average time/residue: 0.3240 time to fit residues: 275.6438 Evaluate side-chains 555 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 391 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 433 PHE Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 139 TRP Chi-restraints excluded: chain C residue 141 TRP Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 431 MET Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 387 ASP Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 141 TRP Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 402 ARG Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 433 PHE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 455 GLN Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 141 TRP Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 402 ARG Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 424 MET Chi-restraints excluded: chain F residue 433 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 441 TYR Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 448 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 181 optimal weight: 7.9990 chunk 100 optimal weight: 40.0000 chunk 207 optimal weight: 10.0000 chunk 168 optimal weight: 40.0000 chunk 0 optimal weight: 60.0000 chunk 124 optimal weight: 7.9990 chunk 218 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 HIS ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS E 73 HIS ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 HIS ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 20826 Z= 0.409 Angle : 0.756 11.838 28218 Z= 0.368 Chirality : 0.047 0.246 2982 Planarity : 0.005 0.047 3690 Dihedral : 9.344 71.648 2895 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 10.19 % Allowed : 31.97 % Favored : 57.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.16), residues: 2526 helix: 0.27 (0.15), residues: 1128 sheet: -1.00 (0.37), residues: 180 loop : -1.91 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 84 HIS 0.004 0.001 HIS B 275 PHE 0.031 0.002 PHE B 230 TYR 0.013 0.002 TYR A 339 ARG 0.008 0.001 ARG B 398 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 426 time to evaluate : 2.111 Fit side-chains revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7645 (mm-30) REVERT: A 75 LEU cc_start: 0.8806 (tp) cc_final: 0.8483 (tp) REVERT: A 84 TRP cc_start: 0.6811 (p-90) cc_final: 0.6324 (p-90) REVERT: A 115 ASN cc_start: 0.8502 (OUTLIER) cc_final: 0.8132 (p0) REVERT: A 132 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7420 (tt) REVERT: A 192 LYS cc_start: -0.0375 (OUTLIER) cc_final: -0.1012 (tptt) REVERT: A 431 MET cc_start: 0.7309 (tpp) cc_final: 0.7041 (tpp) REVERT: A 441 TYR cc_start: 0.7605 (OUTLIER) cc_final: 0.6670 (m-80) REVERT: B 30 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7681 (mtmt) REVERT: B 37 MET cc_start: 0.7826 (ptp) cc_final: 0.7488 (ptp) REVERT: B 44 GLN cc_start: 0.7801 (mm-40) cc_final: 0.7515 (mm-40) REVERT: B 172 TYR cc_start: 0.3633 (OUTLIER) cc_final: 0.3312 (t80) REVERT: B 216 ASN cc_start: 0.7306 (OUTLIER) cc_final: 0.6537 (p0) REVERT: B 346 SER cc_start: 0.8665 (t) cc_final: 0.8447 (m) REVERT: B 373 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7352 (tm-30) REVERT: B 400 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7348 (ttm-80) REVERT: C 57 ARG cc_start: 0.8330 (tpt-90) cc_final: 0.7315 (tpt-90) REVERT: C 76 MET cc_start: 0.8521 (tmm) cc_final: 0.8051 (tmm) REVERT: C 84 TRP cc_start: 0.6707 (p-90) cc_final: 0.6213 (p-90) REVERT: C 137 MET cc_start: 0.7242 (mpp) cc_final: 0.6625 (mpp) REVERT: C 139 TRP cc_start: 0.6471 (OUTLIER) cc_final: 0.5646 (m100) REVERT: C 218 GLU cc_start: 0.6545 (tt0) cc_final: 0.6205 (mt-10) REVERT: C 400 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7568 (ttm-80) REVERT: C 402 ARG cc_start: 0.7616 (mmm-85) cc_final: 0.7367 (mmt180) REVERT: C 459 GLN cc_start: 0.3203 (OUTLIER) cc_final: 0.1742 (pp30) REVERT: D 84 TRP cc_start: 0.6689 (p-90) cc_final: 0.6191 (p-90) REVERT: D 145 MET cc_start: 0.5394 (mmt) cc_final: 0.5058 (mmm) REVERT: D 168 LYS cc_start: 0.6855 (mmpt) cc_final: 0.6624 (mmpt) REVERT: D 373 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7506 (mt-10) REVERT: E 57 ARG cc_start: 0.8535 (tpt-90) cc_final: 0.8324 (tpp-160) REVERT: E 76 MET cc_start: 0.8594 (tmt) cc_final: 0.8242 (tmm) REVERT: E 84 TRP cc_start: 0.7197 (p-90) cc_final: 0.6544 (p-90) REVERT: E 115 ASN cc_start: 0.8526 (OUTLIER) cc_final: 0.8318 (p0) REVERT: E 135 MET cc_start: 0.7233 (tpt) cc_final: 0.6063 (mtt) REVERT: E 141 TRP cc_start: 0.5586 (OUTLIER) cc_final: 0.3937 (t-100) REVERT: E 145 MET cc_start: 0.6385 (mmm) cc_final: 0.5963 (mmt) REVERT: E 192 LYS cc_start: -0.0803 (OUTLIER) cc_final: -0.1426 (tptt) REVERT: E 400 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7201 (ttm-80) REVERT: F 138 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7829 (ttpp) REVERT: F 141 TRP cc_start: 0.5751 (OUTLIER) cc_final: 0.4381 (t-100) REVERT: F 145 MET cc_start: 0.6374 (mmm) cc_final: 0.6138 (mmm) REVERT: F 373 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7306 (mt-10) REVERT: F 381 LYS cc_start: 0.7767 (pttt) cc_final: 0.7361 (pttt) REVERT: F 400 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7026 (ttm-80) REVERT: F 433 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7466 (t80) REVERT: F 441 TYR cc_start: 0.7705 (OUTLIER) cc_final: 0.7350 (m-80) outliers start: 217 outliers final: 158 residues processed: 587 average time/residue: 0.3166 time to fit residues: 282.0731 Evaluate side-chains 583 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 402 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 433 PHE Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 139 TRP Chi-restraints excluded: chain C residue 141 TRP Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 387 ASP Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 141 TRP Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 400 ARG Chi-restraints excluded: chain E residue 402 ARG Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 433 PHE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 138 LYS Chi-restraints excluded: chain F residue 141 TRP Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 359 LYS Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 396 SER Chi-restraints excluded: chain F residue 400 ARG Chi-restraints excluded: chain F residue 402 ARG Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 424 MET Chi-restraints excluded: chain F residue 433 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 441 TYR Chi-restraints excluded: chain F residue 445 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 10.0000 chunk 219 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 143 optimal weight: 0.1980 chunk 60 optimal weight: 30.0000 chunk 243 optimal weight: 0.0570 chunk 202 optimal weight: 0.5980 chunk 112 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 overall best weight: 1.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 HIS ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS E 73 HIS E 201 ASN ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20826 Z= 0.166 Angle : 0.633 13.590 28218 Z= 0.299 Chirality : 0.042 0.312 2982 Planarity : 0.004 0.039 3690 Dihedral : 8.142 59.656 2890 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 7.18 % Allowed : 34.79 % Favored : 58.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.57 (0.17), residues: 2526 helix: 1.10 (0.16), residues: 1110 sheet: -0.78 (0.36), residues: 240 loop : -1.80 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 84 HIS 0.005 0.001 HIS B 224 PHE 0.034 0.001 PHE A 230 TYR 0.012 0.001 TYR C 441 ARG 0.005 0.000 ARG B 398 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 403 time to evaluate : 2.282 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.8148 (ptp) cc_final: 0.7552 (ptp) REVERT: A 44 GLN cc_start: 0.7639 (mm-40) cc_final: 0.7351 (mm-40) REVERT: A 45 ILE cc_start: 0.8727 (mt) cc_final: 0.7688 (mt) REVERT: A 49 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7889 (mp0) REVERT: A 75 LEU cc_start: 0.8812 (tp) cc_final: 0.8535 (tp) REVERT: A 115 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.8011 (p0) REVERT: A 132 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7299 (tt) REVERT: B 30 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7782 (mtmt) REVERT: B 37 MET cc_start: 0.7774 (ptp) cc_final: 0.7426 (ptp) REVERT: B 49 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: B 150 LYS cc_start: 0.8971 (mmpt) cc_final: 0.8204 (tmtt) REVERT: B 216 ASN cc_start: 0.7356 (OUTLIER) cc_final: 0.7017 (p0) REVERT: B 346 SER cc_start: 0.8560 (t) cc_final: 0.8247 (m) REVERT: B 383 LYS cc_start: 0.5529 (OUTLIER) cc_final: 0.4610 (mtpp) REVERT: B 400 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7300 (ttm-80) REVERT: C 57 ARG cc_start: 0.8268 (tpt-90) cc_final: 0.7619 (tpt-90) REVERT: C 76 MET cc_start: 0.8541 (tmm) cc_final: 0.7905 (tmm) REVERT: C 78 LEU cc_start: 0.9086 (tm) cc_final: 0.8754 (mm) REVERT: C 139 TRP cc_start: 0.6429 (OUTLIER) cc_final: 0.5564 (m100) REVERT: C 169 PHE cc_start: 0.8471 (t80) cc_final: 0.8241 (t80) REVERT: C 373 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6988 (mt-10) REVERT: C 402 ARG cc_start: 0.7481 (mmm-85) cc_final: 0.7200 (mmt180) REVERT: D 168 LYS cc_start: 0.6755 (mmpt) cc_final: 0.6479 (mmpt) REVERT: E 76 MET cc_start: 0.8361 (tmt) cc_final: 0.8078 (tmm) REVERT: E 84 TRP cc_start: 0.7152 (p-90) cc_final: 0.6537 (p-90) REVERT: E 135 MET cc_start: 0.7173 (tpt) cc_final: 0.6228 (mtt) REVERT: E 141 TRP cc_start: 0.5180 (OUTLIER) cc_final: 0.3328 (t-100) REVERT: E 145 MET cc_start: 0.6213 (mmm) cc_final: 0.5822 (mmt) REVERT: E 150 LYS cc_start: 0.9041 (mmmt) cc_final: 0.8538 (tmtt) REVERT: E 154 LYS cc_start: 0.4802 (OUTLIER) cc_final: 0.4491 (tttm) REVERT: E 192 LYS cc_start: -0.0493 (OUTLIER) cc_final: -0.1171 (tptt) REVERT: E 373 GLU cc_start: 0.7595 (mm-30) cc_final: 0.6917 (mt-10) REVERT: F 141 TRP cc_start: 0.5417 (OUTLIER) cc_final: 0.3855 (t-100) REVERT: F 150 LYS cc_start: 0.8874 (mppt) cc_final: 0.8277 (tttt) REVERT: F 373 GLU cc_start: 0.7714 (mm-30) cc_final: 0.6918 (mt-10) REVERT: F 381 LYS cc_start: 0.7441 (pttt) cc_final: 0.7210 (pttt) REVERT: F 416 THR cc_start: 0.6467 (OUTLIER) cc_final: 0.6255 (m) REVERT: F 441 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.7284 (m-80) outliers start: 153 outliers final: 102 residues processed: 518 average time/residue: 0.3420 time to fit residues: 266.4455 Evaluate side-chains 508 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 391 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 433 PHE Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 139 TRP Chi-restraints excluded: chain C residue 141 TRP Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 431 MET Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 387 ASP Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 141 TRP Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 154 LYS Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 284 CYS Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 402 ARG Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 433 PHE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain F residue 141 TRP Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 402 ARG Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 424 MET Chi-restraints excluded: chain F residue 433 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 441 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 178 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 205 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 242 optimal weight: 2.9990 chunk 152 optimal weight: 8.9990 chunk 148 optimal weight: 20.0000 chunk 112 optimal weight: 40.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 HIS ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS D 109 HIS D 156 ASN E 73 HIS E 201 ASN ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20826 Z= 0.187 Angle : 0.641 12.284 28218 Z= 0.297 Chirality : 0.042 0.321 2982 Planarity : 0.004 0.039 3690 Dihedral : 7.755 65.956 2866 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 7.18 % Allowed : 34.74 % Favored : 58.08 % 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 (0.17), residues: 2526 helix: 1.20 (0.16), residues: 1116 sheet: -0.74 (0.36), residues: 240 loop : -1.69 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 84 HIS 0.003 0.001 HIS C 224 PHE 0.033 0.002 PHE D 230 TYR 0.016 0.001 TYR B 328 ARG 0.005 0.000 ARG B 398 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 406 time to evaluate : 2.435 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.8215 (ptp) cc_final: 0.7626 (ptp) REVERT: A 45 ILE cc_start: 0.8777 (mt) cc_final: 0.7626 (mt) REVERT: A 49 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: A 75 LEU cc_start: 0.8824 (tp) cc_final: 0.8540 (tp) REVERT: A 115 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.7985 (p0) REVERT: A 132 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7331 (tt) REVERT: A 150 LYS cc_start: 0.8772 (mppt) cc_final: 0.8279 (tmtt) REVERT: B 30 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7762 (mtmt) REVERT: B 37 MET cc_start: 0.7745 (ptp) cc_final: 0.7427 (ptp) REVERT: B 45 ILE cc_start: 0.8705 (mt) cc_final: 0.7466 (mp) REVERT: B 49 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: B 150 LYS cc_start: 0.8916 (mmpt) cc_final: 0.8193 (tmtt) REVERT: B 216 ASN cc_start: 0.7152 (OUTLIER) cc_final: 0.6727 (p0) REVERT: B 346 SER cc_start: 0.8602 (t) cc_final: 0.8261 (m) REVERT: B 373 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7467 (tm-30) REVERT: B 381 LYS cc_start: 0.6940 (ptpt) cc_final: 0.5901 (pttt) REVERT: B 383 LYS cc_start: 0.5702 (OUTLIER) cc_final: 0.4776 (mtpp) REVERT: B 384 ASP cc_start: 0.6910 (t0) cc_final: 0.6638 (t0) REVERT: B 400 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7300 (ttm-80) REVERT: C 76 MET cc_start: 0.8601 (tmm) cc_final: 0.7959 (tmm) REVERT: C 78 LEU cc_start: 0.9093 (tm) cc_final: 0.8659 (mm) REVERT: C 139 TRP cc_start: 0.6445 (OUTLIER) cc_final: 0.5632 (m100) REVERT: C 348 GLN cc_start: 0.7946 (mt0) cc_final: 0.7740 (tt0) REVERT: C 363 TYR cc_start: 0.7215 (m-10) cc_final: 0.6992 (m-80) REVERT: C 373 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7023 (mt-10) REVERT: C 402 ARG cc_start: 0.7561 (mmm-85) cc_final: 0.7285 (mmt180) REVERT: C 459 GLN cc_start: 0.3250 (OUTLIER) cc_final: 0.1854 (pp30) REVERT: D 168 LYS cc_start: 0.6616 (mmpt) cc_final: 0.6379 (mmpt) REVERT: D 176 GLU cc_start: 0.5799 (OUTLIER) cc_final: 0.5363 (tt0) REVERT: E 76 MET cc_start: 0.8372 (tmt) cc_final: 0.8127 (tmm) REVERT: E 84 TRP cc_start: 0.7207 (p-90) cc_final: 0.6556 (p-90) REVERT: E 135 MET cc_start: 0.7247 (tpt) cc_final: 0.6246 (mtt) REVERT: E 141 TRP cc_start: 0.5365 (OUTLIER) cc_final: 0.3624 (t-100) REVERT: E 150 LYS cc_start: 0.8983 (mmmt) cc_final: 0.8463 (tmtt) REVERT: E 154 LYS cc_start: 0.4670 (OUTLIER) cc_final: 0.4463 (tttm) REVERT: E 192 LYS cc_start: -0.0766 (OUTLIER) cc_final: -0.1311 (tptt) REVERT: E 373 GLU cc_start: 0.7681 (mm-30) cc_final: 0.6990 (mt-10) REVERT: F 141 TRP cc_start: 0.5444 (OUTLIER) cc_final: 0.3916 (t-100) REVERT: F 145 MET cc_start: 0.6348 (mmm) cc_final: 0.6058 (mmt) REVERT: F 150 LYS cc_start: 0.8762 (mppt) cc_final: 0.8268 (tmtt) REVERT: F 373 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7115 (mt-10) REVERT: F 381 LYS cc_start: 0.7428 (pttt) cc_final: 0.7193 (pttt) REVERT: F 400 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7052 (ttm-80) REVERT: F 416 THR cc_start: 0.6545 (OUTLIER) cc_final: 0.6341 (m) REVERT: F 441 TYR cc_start: 0.7711 (OUTLIER) cc_final: 0.7450 (m-80) outliers start: 153 outliers final: 118 residues processed: 525 average time/residue: 0.3245 time to fit residues: 257.4248 Evaluate side-chains 531 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 394 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 433 PHE Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 139 TRP Chi-restraints excluded: chain C residue 141 TRP Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 387 ASP Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 141 TRP Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 154 LYS Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 402 ARG Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 433 PHE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain F residue 141 TRP Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 400 ARG Chi-restraints excluded: chain F residue 402 ARG Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 424 MET Chi-restraints excluded: chain F residue 433 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 441 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 0.0470 chunk 96 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 190 optimal weight: 9.9990 chunk 220 optimal weight: 4.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN C 201 ASN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN E 73 HIS E 201 ASN ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20826 Z= 0.188 Angle : 0.643 12.804 28218 Z= 0.298 Chirality : 0.042 0.324 2982 Planarity : 0.004 0.037 3690 Dihedral : 7.666 67.873 2866 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 7.98 % Allowed : 33.90 % Favored : 58.12 % 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: -0.32 (0.17), residues: 2526 helix: 1.34 (0.16), residues: 1110 sheet: -0.72 (0.36), residues: 240 loop : -1.68 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 84 HIS 0.004 0.001 HIS E 73 PHE 0.034 0.001 PHE D 230 TYR 0.014 0.001 TYR B 328 ARG 0.005 0.000 ARG B 398 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 401 time to evaluate : 2.298 Fit side-chains revert: symmetry clash REVERT: A 14 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6331 (pp) REVERT: A 37 MET cc_start: 0.8248 (ptp) cc_final: 0.7666 (ptp) REVERT: A 45 ILE cc_start: 0.8775 (mt) cc_final: 0.7577 (mt) REVERT: A 49 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: A 75 LEU cc_start: 0.8825 (tp) cc_final: 0.8552 (tp) REVERT: A 115 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.7932 (p0) REVERT: A 132 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7327 (tt) REVERT: A 150 LYS cc_start: 0.8726 (mppt) cc_final: 0.8284 (tmtt) REVERT: B 30 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7739 (mtmt) REVERT: B 37 MET cc_start: 0.7733 (ptp) cc_final: 0.7403 (ptp) REVERT: B 45 ILE cc_start: 0.8736 (mt) cc_final: 0.7307 (mp) REVERT: B 49 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: B 150 LYS cc_start: 0.8878 (mmpt) cc_final: 0.8174 (tptt) REVERT: B 216 ASN cc_start: 0.7165 (OUTLIER) cc_final: 0.6770 (p0) REVERT: B 346 SER cc_start: 0.8600 (t) cc_final: 0.8255 (m) REVERT: B 373 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: B 383 LYS cc_start: 0.5684 (OUTLIER) cc_final: 0.4906 (mtpp) REVERT: B 384 ASP cc_start: 0.6893 (t0) cc_final: 0.6647 (t0) REVERT: B 400 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7281 (ttm-80) REVERT: C 76 MET cc_start: 0.8606 (tmm) cc_final: 0.7957 (tmm) REVERT: C 78 LEU cc_start: 0.9082 (tm) cc_final: 0.8654 (mm) REVERT: C 139 TRP cc_start: 0.6550 (OUTLIER) cc_final: 0.5550 (m100) REVERT: C 348 GLN cc_start: 0.7977 (mt0) cc_final: 0.7737 (tt0) REVERT: C 373 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7071 (mt-10) REVERT: C 400 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.6536 (ttm-80) REVERT: C 402 ARG cc_start: 0.7564 (mmm-85) cc_final: 0.7284 (mmt180) REVERT: C 459 GLN cc_start: 0.3242 (OUTLIER) cc_final: 0.1832 (pp30) REVERT: D 48 ASP cc_start: 0.6930 (OUTLIER) cc_final: 0.6411 (m-30) REVERT: D 168 LYS cc_start: 0.6640 (mmpt) cc_final: 0.6395 (mmpt) REVERT: E 76 MET cc_start: 0.8382 (tmt) cc_final: 0.8103 (tmm) REVERT: E 84 TRP cc_start: 0.7210 (p-90) cc_final: 0.6556 (p-90) REVERT: E 135 MET cc_start: 0.7223 (tpt) cc_final: 0.6217 (mtt) REVERT: E 141 TRP cc_start: 0.5373 (OUTLIER) cc_final: 0.4318 (t60) REVERT: E 150 LYS cc_start: 0.8968 (mmmt) cc_final: 0.8458 (tmtt) REVERT: E 192 LYS cc_start: -0.0785 (OUTLIER) cc_final: -0.1318 (tptt) REVERT: E 373 GLU cc_start: 0.7586 (mm-30) cc_final: 0.6871 (mt-10) REVERT: E 400 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7116 (ttm-80) REVERT: E 455 GLN cc_start: 0.6310 (OUTLIER) cc_final: 0.5720 (mt0) REVERT: F 141 TRP cc_start: 0.5379 (OUTLIER) cc_final: 0.3864 (t-100) REVERT: F 145 MET cc_start: 0.6306 (mmm) cc_final: 0.5998 (mmt) REVERT: F 150 LYS cc_start: 0.8714 (mppt) cc_final: 0.8265 (tmtt) REVERT: F 373 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7074 (mt-10) REVERT: F 381 LYS cc_start: 0.7346 (pttt) cc_final: 0.7103 (pttt) REVERT: F 400 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7055 (ttm-80) REVERT: F 416 THR cc_start: 0.6574 (OUTLIER) cc_final: 0.6373 (m) REVERT: F 441 TYR cc_start: 0.7685 (OUTLIER) cc_final: 0.7454 (m-80) outliers start: 170 outliers final: 132 residues processed: 530 average time/residue: 0.3295 time to fit residues: 263.1383 Evaluate side-chains 548 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 394 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 433 PHE Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 139 TRP Chi-restraints excluded: chain C residue 141 TRP Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 387 ASP Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 31 ARG Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 141 TRP Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 284 CYS Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 400 ARG Chi-restraints excluded: chain E residue 402 ARG Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 433 PHE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 455 GLN Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain F residue 141 TRP Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 400 ARG Chi-restraints excluded: chain F residue 402 ARG Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 424 MET Chi-restraints excluded: chain F residue 433 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 441 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 4.9990 chunk 212 optimal weight: 0.9980 chunk 226 optimal weight: 20.0000 chunk 136 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 177 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 214 optimal weight: 8.9990 chunk 225 optimal weight: 30.0000 chunk 148 optimal weight: 0.1980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN C 231 GLN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN E 73 HIS E 201 ASN ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20826 Z= 0.189 Angle : 0.641 12.458 28218 Z= 0.297 Chirality : 0.042 0.299 2982 Planarity : 0.004 0.036 3690 Dihedral : 7.618 70.114 2866 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 7.79 % Allowed : 33.76 % Favored : 58.45 % 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: -0.24 (0.17), residues: 2526 helix: 1.41 (0.16), residues: 1110 sheet: -0.92 (0.32), residues: 294 loop : -1.58 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 84 HIS 0.004 0.001 HIS E 73 PHE 0.033 0.001 PHE D 230 TYR 0.013 0.001 TYR B 328 ARG 0.005 0.000 ARG B 398 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 395 time to evaluate : 2.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.6166 (pp) REVERT: A 31 ARG cc_start: 0.7813 (tpp80) cc_final: 0.7499 (mmp80) REVERT: A 37 MET cc_start: 0.8230 (ptp) cc_final: 0.7626 (ptp) REVERT: A 45 ILE cc_start: 0.8792 (mt) cc_final: 0.7617 (mt) REVERT: A 49 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: A 75 LEU cc_start: 0.8839 (tp) cc_final: 0.8573 (tp) REVERT: A 115 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.7909 (p0) REVERT: B 30 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7763 (mtmt) REVERT: B 37 MET cc_start: 0.7736 (ptp) cc_final: 0.7408 (ptp) REVERT: B 45 ILE cc_start: 0.8702 (mt) cc_final: 0.7313 (mp) REVERT: B 48 ASP cc_start: 0.6483 (OUTLIER) cc_final: 0.5790 (m-30) REVERT: B 49 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: B 145 MET cc_start: 0.5123 (mmm) cc_final: 0.4655 (mmm) REVERT: B 150 LYS cc_start: 0.8856 (mmpt) cc_final: 0.8179 (tptt) REVERT: B 216 ASN cc_start: 0.7134 (OUTLIER) cc_final: 0.6770 (p0) REVERT: B 346 SER cc_start: 0.8598 (t) cc_final: 0.8248 (m) REVERT: B 373 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7388 (tm-30) REVERT: B 383 LYS cc_start: 0.5563 (OUTLIER) cc_final: 0.4630 (mtpp) REVERT: B 400 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7279 (ttm-80) REVERT: C 76 MET cc_start: 0.8611 (tmm) cc_final: 0.8255 (tmm) REVERT: C 78 LEU cc_start: 0.9083 (tm) cc_final: 0.8648 (mm) REVERT: C 137 MET cc_start: 0.7385 (mpp) cc_final: 0.6900 (mpp) REVERT: C 139 TRP cc_start: 0.6453 (OUTLIER) cc_final: 0.5547 (m100) REVERT: C 348 GLN cc_start: 0.7964 (mt0) cc_final: 0.7732 (tt0) REVERT: C 373 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7070 (mt-10) REVERT: C 400 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.6534 (ttm-80) REVERT: C 402 ARG cc_start: 0.7563 (mmm-85) cc_final: 0.7281 (mmt180) REVERT: C 459 GLN cc_start: 0.3250 (OUTLIER) cc_final: 0.1840 (pp30) REVERT: D 48 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.6523 (m-30) REVERT: D 168 LYS cc_start: 0.6636 (mmpt) cc_final: 0.6361 (mmpt) REVERT: D 348 GLN cc_start: 0.7917 (mt0) cc_final: 0.7693 (tt0) REVERT: E 76 MET cc_start: 0.8546 (tmt) cc_final: 0.8244 (tmm) REVERT: E 84 TRP cc_start: 0.7202 (p-90) cc_final: 0.6531 (p-90) REVERT: E 135 MET cc_start: 0.7228 (tpt) cc_final: 0.6215 (mtt) REVERT: E 141 TRP cc_start: 0.5344 (OUTLIER) cc_final: 0.3597 (t-100) REVERT: E 150 LYS cc_start: 0.8956 (mmmt) cc_final: 0.8496 (tmtt) REVERT: E 192 LYS cc_start: -0.0810 (OUTLIER) cc_final: -0.1333 (tptt) REVERT: E 400 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7069 (ttm-80) REVERT: E 455 GLN cc_start: 0.6299 (OUTLIER) cc_final: 0.5699 (mt0) REVERT: F 141 TRP cc_start: 0.5361 (OUTLIER) cc_final: 0.3866 (t-100) REVERT: F 145 MET cc_start: 0.6216 (mmm) cc_final: 0.5965 (mmt) REVERT: F 373 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7045 (mt-10) REVERT: F 381 LYS cc_start: 0.7304 (pttt) cc_final: 0.7080 (pttt) REVERT: F 400 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7079 (ttm-80) REVERT: F 441 TYR cc_start: 0.7686 (OUTLIER) cc_final: 0.7431 (m-80) outliers start: 166 outliers final: 135 residues processed: 521 average time/residue: 0.3284 time to fit residues: 257.7207 Evaluate side-chains 549 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 393 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 433 PHE Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 139 TRP Chi-restraints excluded: chain C residue 141 TRP Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 431 MET Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 387 ASP Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain E residue 31 ARG Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 141 TRP Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 400 ARG Chi-restraints excluded: chain E residue 402 ARG Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 433 PHE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 455 GLN Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain F residue 141 TRP Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 400 ARG Chi-restraints excluded: chain F residue 402 ARG Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 424 MET Chi-restraints excluded: chain F residue 433 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 441 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 251 optimal weight: 20.0000 chunk 231 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 154 optimal weight: 30.0000 chunk 122 optimal weight: 10.0000 chunk 158 optimal weight: 0.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 HIS ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN E 73 HIS F 58 GLN ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20826 Z= 0.275 Angle : 0.685 12.166 28218 Z= 0.321 Chirality : 0.044 0.283 2982 Planarity : 0.004 0.038 3690 Dihedral : 7.873 73.677 2866 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 7.23 % Allowed : 34.18 % Favored : 58.59 % 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: -0.41 (0.17), residues: 2526 helix: 1.22 (0.15), residues: 1110 sheet: -0.78 (0.35), residues: 240 loop : -1.68 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 84 HIS 0.004 0.001 HIS E 73 PHE 0.032 0.002 PHE D 230 TYR 0.013 0.001 TYR B 328 ARG 0.005 0.000 ARG B 398 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 393 time to evaluate : 2.270 Fit side-chains revert: symmetry clash REVERT: A 14 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6532 (pp) REVERT: A 31 ARG cc_start: 0.7992 (tpp80) cc_final: 0.7687 (mmp80) REVERT: A 37 MET cc_start: 0.8295 (ptp) cc_final: 0.7772 (ptp) REVERT: A 45 ILE cc_start: 0.8697 (mt) cc_final: 0.7581 (mt) REVERT: A 49 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7694 (mp0) REVERT: A 75 LEU cc_start: 0.8865 (tp) cc_final: 0.8598 (tp) REVERT: A 115 ASN cc_start: 0.8247 (p0) cc_final: 0.7936 (p0) REVERT: B 30 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7778 (mtmt) REVERT: B 37 MET cc_start: 0.7778 (ptp) cc_final: 0.7523 (ptp) REVERT: B 49 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7417 (mm-30) REVERT: B 145 MET cc_start: 0.5248 (mmm) cc_final: 0.4801 (mmm) REVERT: B 216 ASN cc_start: 0.7223 (OUTLIER) cc_final: 0.6819 (p0) REVERT: B 346 SER cc_start: 0.8669 (t) cc_final: 0.8334 (m) REVERT: B 373 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7296 (tm-30) REVERT: B 400 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7427 (ttm-80) REVERT: C 76 MET cc_start: 0.8601 (tmm) cc_final: 0.8242 (tmm) REVERT: C 78 LEU cc_start: 0.9091 (tm) cc_final: 0.8669 (mm) REVERT: C 139 TRP cc_start: 0.6369 (OUTLIER) cc_final: 0.5441 (m100) REVERT: C 400 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.6494 (ttm-80) REVERT: C 402 ARG cc_start: 0.7612 (mmm-85) cc_final: 0.7358 (mmt180) REVERT: C 459 GLN cc_start: 0.3158 (OUTLIER) cc_final: 0.1727 (pp30) REVERT: D 76 MET cc_start: 0.8708 (ttp) cc_final: 0.8427 (tmm) REVERT: D 168 LYS cc_start: 0.6629 (mmpt) cc_final: 0.6384 (mmpt) REVERT: E 76 MET cc_start: 0.8634 (tmt) cc_final: 0.8296 (tmm) REVERT: E 84 TRP cc_start: 0.7267 (p-90) cc_final: 0.6892 (p-90) REVERT: E 135 MET cc_start: 0.7124 (tpt) cc_final: 0.6213 (mtt) REVERT: E 139 TRP cc_start: 0.6157 (m-10) cc_final: 0.5725 (m100) REVERT: E 141 TRP cc_start: 0.5548 (OUTLIER) cc_final: 0.3828 (t-100) REVERT: E 150 LYS cc_start: 0.8972 (mmmt) cc_final: 0.8499 (tmtt) REVERT: E 192 LYS cc_start: -0.0809 (OUTLIER) cc_final: -0.1359 (tptt) REVERT: E 373 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7086 (mt-10) REVERT: E 400 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7115 (ttm-80) REVERT: E 432 ASP cc_start: 0.7057 (OUTLIER) cc_final: 0.6751 (p0) REVERT: F 141 TRP cc_start: 0.5538 (OUTLIER) cc_final: 0.4050 (t-100) REVERT: F 150 LYS cc_start: 0.8715 (mppt) cc_final: 0.8256 (tmtt) REVERT: F 373 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7199 (mt-10) REVERT: F 381 LYS cc_start: 0.7467 (pttt) cc_final: 0.7183 (pttt) REVERT: F 400 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7095 (ttm-80) REVERT: F 432 ASP cc_start: 0.6994 (OUTLIER) cc_final: 0.6758 (p0) outliers start: 154 outliers final: 132 residues processed: 514 average time/residue: 0.3501 time to fit residues: 273.1347 Evaluate side-chains 533 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 384 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 433 PHE Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 139 TRP Chi-restraints excluded: chain C residue 141 TRP Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 387 ASP Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain E residue 31 ARG Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 141 TRP Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 400 ARG Chi-restraints excluded: chain E residue 402 ARG Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 424 MET Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 433 PHE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain F residue 141 TRP Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 400 ARG Chi-restraints excluded: chain F residue 402 ARG Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 424 MET Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 433 PHE Chi-restraints excluded: chain F residue 438 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 7.9990 chunk 61 optimal weight: 20.0000 chunk 184 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 chunk 83 optimal weight: 0.5980 chunk 205 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 175 optimal weight: 9.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 HIS ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS D 156 ASN E 73 HIS E 201 ASN ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.200933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.163373 restraints weight = 25928.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.167549 restraints weight = 16659.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.170265 restraints weight = 12750.989| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20826 Z= 0.279 Angle : 0.697 14.792 28218 Z= 0.327 Chirality : 0.044 0.281 2982 Planarity : 0.004 0.040 3690 Dihedral : 7.863 72.789 2862 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 7.46 % Allowed : 34.04 % Favored : 58.50 % 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: -0.48 (0.17), residues: 2526 helix: 1.13 (0.15), residues: 1110 sheet: -0.88 (0.34), residues: 240 loop : -1.67 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 139 HIS 0.004 0.001 HIS E 73 PHE 0.032 0.002 PHE E 230 TYR 0.013 0.001 TYR B 328 ARG 0.006 0.000 ARG B 398 =============================================================================== Job complete usr+sys time: 4936.35 seconds wall clock time: 89 minutes 43.78 seconds (5383.78 seconds total)