Starting phenix.real_space_refine on Wed Feb 14 19:13:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5t_24839/02_2024/7s5t_24839.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5t_24839/02_2024/7s5t_24839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5t_24839/02_2024/7s5t_24839.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5t_24839/02_2024/7s5t_24839.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5t_24839/02_2024/7s5t_24839.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5t_24839/02_2024/7s5t_24839.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 64 5.16 5 C 6488 2.51 5 N 1720 2.21 5 O 1804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 32": "NH1" <-> "NH2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 65": "OD1" <-> "OD2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 99": "OD1" <-> "OD2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ASP 237": "OD1" <-> "OD2" Residue "A ASP 262": "OD1" <-> "OD2" Residue "A ASP 280": "OD1" <-> "OD2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A ASP 323": "OD1" <-> "OD2" Residue "A TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "A GLU 351": "OE1" <-> "OE2" Residue "A ASP 352": "OD1" <-> "OD2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B GLU 179": "OE1" <-> "OE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B ASP 237": "OD1" <-> "OD2" Residue "B ASP 262": "OD1" <-> "OD2" Residue "B ASP 280": "OD1" <-> "OD2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B GLU 322": "OE1" <-> "OE2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "B TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 350": "OD1" <-> "OD2" Residue "B GLU 351": "OE1" <-> "OE2" Residue "B ASP 352": "OD1" <-> "OD2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 51": "OE1" <-> "OE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 65": "OD1" <-> "OD2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "C GLU 141": "OE1" <-> "OE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C ASP 237": "OD1" <-> "OD2" Residue "C ASP 262": "OD1" <-> "OD2" Residue "C ASP 280": "OD1" <-> "OD2" Residue "C GLU 282": "OE1" <-> "OE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C GLU 321": "OE1" <-> "OE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "C ASP 323": "OD1" <-> "OD2" Residue "C TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 350": "OD1" <-> "OD2" Residue "C GLU 351": "OE1" <-> "OE2" Residue "C ASP 352": "OD1" <-> "OD2" Residue "D ARG 32": "NH1" <-> "NH2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 65": "OD1" <-> "OD2" Residue "D PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 195": "NH1" <-> "NH2" Residue "D ASP 237": "OD1" <-> "OD2" Residue "D ASP 262": "OD1" <-> "OD2" Residue "D ASP 280": "OD1" <-> "OD2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "D GLU 321": "OE1" <-> "OE2" Residue "D GLU 322": "OE1" <-> "OE2" Residue "D ASP 323": "OD1" <-> "OD2" Residue "D TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 350": "OD1" <-> "OD2" Residue "D GLU 351": "OE1" <-> "OE2" Residue "D ASP 352": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10078 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain: "B" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain: "C" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain: "D" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.71, per 1000 atoms: 0.57 Number of scatterers: 10078 At special positions: 0 Unit cell: (91, 89.7, 122.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 2 19.00 S 64 16.00 O 1804 8.00 N 1720 7.00 C 6488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.03 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: 3.62 Conformation dependent library (CDL) restraints added in 1.7 seconds 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2416 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 20 sheets defined 34.8% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 51 through 57 removed outlier: 3.783A pdb=" N ARG A 54 " --> pdb=" O GLU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 65 removed outlier: 3.670A pdb=" N THR A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 97 Processing helix chain 'A' and resid 116 through 129 Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.557A pdb=" N ILE A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 removed outlier: 4.042A pdb=" N ARG A 176 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA A 178 " --> pdb=" O HIS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.809A pdb=" N LEU A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 333 Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'B' and resid 51 through 57 removed outlier: 3.783A pdb=" N ARG B 54 " --> pdb=" O GLU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 65 removed outlier: 3.670A pdb=" N THR B 62 " --> pdb=" O ASP B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 97 Processing helix chain 'B' and resid 116 through 129 Processing helix chain 'B' and resid 142 through 172 removed outlier: 3.557A pdb=" N ILE B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 removed outlier: 4.042A pdb=" N ARG B 176 " --> pdb=" O GLN B 173 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA B 178 " --> pdb=" O HIS B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.809A pdb=" N LEU B 275 " --> pdb=" O PRO B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 333 Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'C' and resid 51 through 57 removed outlier: 3.784A pdb=" N ARG C 54 " --> pdb=" O GLU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 65 removed outlier: 3.668A pdb=" N THR C 62 " --> pdb=" O ASP C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 97 Processing helix chain 'C' and resid 116 through 129 Processing helix chain 'C' and resid 142 through 172 removed outlier: 3.558A pdb=" N ILE C 146 " --> pdb=" O CYS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 179 removed outlier: 4.042A pdb=" N ARG C 176 " --> pdb=" O GLN C 173 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA C 178 " --> pdb=" O HIS C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 333 Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'D' and resid 51 through 57 removed outlier: 3.783A pdb=" N ARG D 54 " --> pdb=" O GLU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 65 removed outlier: 3.669A pdb=" N THR D 62 " --> pdb=" O ASP D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 97 Processing helix chain 'D' and resid 116 through 129 Processing helix chain 'D' and resid 142 through 172 removed outlier: 3.557A pdb=" N ILE D 146 " --> pdb=" O CYS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 179 removed outlier: 4.042A pdb=" N ARG D 176 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA D 178 " --> pdb=" O HIS D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 275 removed outlier: 3.810A pdb=" N LEU D 275 " --> pdb=" O PRO D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 333 Processing helix chain 'D' and resid 346 through 351 Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 removed outlier: 6.773A pdb=" N ALA A 187 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 230 through 238 removed outlier: 5.064A pdb=" N THR A 223 " --> pdb=" O PRO A 232 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA A 213 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLU A 288 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE A 215 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE A 286 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N MET A 217 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE A 284 " --> pdb=" O MET A 217 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N VAL A 219 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLU A 282 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 315 Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 322 Processing sheet with id=AA6, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'B' and resid 181 through 183 removed outlier: 6.773A pdb=" N ALA B 187 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 230 through 238 removed outlier: 5.064A pdb=" N THR B 223 " --> pdb=" O PRO B 232 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET B 217 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA B 213 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLU B 288 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE B 215 " --> pdb=" O ILE B 286 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE B 286 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N MET B 217 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE B 284 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL B 219 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLU B 282 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 313 through 315 Processing sheet with id=AB1, first strand: chain 'B' and resid 319 through 322 Processing sheet with id=AB2, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AB3, first strand: chain 'C' and resid 181 through 183 removed outlier: 6.774A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 230 through 238 removed outlier: 5.064A pdb=" N THR C 223 " --> pdb=" O PRO C 232 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA C 213 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLU C 288 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE C 215 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE C 286 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N MET C 217 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE C 284 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL C 219 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU C 282 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 313 through 315 Processing sheet with id=AB6, first strand: chain 'C' and resid 319 through 322 Processing sheet with id=AB7, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AB8, first strand: chain 'D' and resid 181 through 183 removed outlier: 6.773A pdb=" N ALA D 187 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 230 through 238 removed outlier: 5.064A pdb=" N THR D 223 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET D 217 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA D 213 " --> pdb=" O GLU D 288 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLU D 288 " --> pdb=" O ALA D 213 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE D 215 " --> pdb=" O ILE D 286 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE D 286 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N MET D 217 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE D 284 " --> pdb=" O MET D 217 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL D 219 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU D 282 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 313 through 315 Processing sheet with id=AC2, first strand: chain 'D' and resid 319 through 322 447 hydrogen bonds defined for protein. 1224 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: 2.96 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3272 1.34 - 1.46: 2071 1.46 - 1.57: 4857 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 10304 Sorted by residual: bond pdb=" CB GLU D 104 " pdb=" CG GLU D 104 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.05e+00 bond pdb=" CB GLU C 104 " pdb=" CG GLU C 104 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.04e+00 bond pdb=" CB GLU B 104 " pdb=" CG GLU B 104 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.03e+00 bond pdb=" CB GLU A 104 " pdb=" CG GLU A 104 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.98e+00 bond pdb=" CG GLU A 104 " pdb=" CD GLU A 104 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.16e+00 ... (remaining 10299 not shown) Histogram of bond angle deviations from ideal: 100.30 - 107.04: 340 107.04 - 113.77: 6039 113.77 - 120.51: 3858 120.51 - 127.24: 3629 127.24 - 133.98: 142 Bond angle restraints: 14008 Sorted by residual: angle pdb=" CB GLU B 104 " pdb=" CG GLU B 104 " pdb=" CD GLU B 104 " ideal model delta sigma weight residual 112.60 118.72 -6.12 1.70e+00 3.46e-01 1.29e+01 angle pdb=" CB GLU C 104 " pdb=" CG GLU C 104 " pdb=" CD GLU C 104 " ideal model delta sigma weight residual 112.60 118.71 -6.11 1.70e+00 3.46e-01 1.29e+01 angle pdb=" CB GLU A 104 " pdb=" CG GLU A 104 " pdb=" CD GLU A 104 " ideal model delta sigma weight residual 112.60 118.71 -6.11 1.70e+00 3.46e-01 1.29e+01 angle pdb=" CB GLU D 104 " pdb=" CG GLU D 104 " pdb=" CD GLU D 104 " ideal model delta sigma weight residual 112.60 118.71 -6.11 1.70e+00 3.46e-01 1.29e+01 angle pdb=" CA GLU C 104 " pdb=" CB GLU C 104 " pdb=" CG GLU C 104 " ideal model delta sigma weight residual 114.10 120.56 -6.46 2.00e+00 2.50e-01 1.04e+01 ... (remaining 14003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 5494 16.98 - 33.95: 446 33.95 - 50.93: 120 50.93 - 67.91: 52 67.91 - 84.88: 16 Dihedral angle restraints: 6128 sinusoidal: 2412 harmonic: 3716 Sorted by residual: dihedral pdb=" CB CYS A 110 " pdb=" SG CYS A 110 " pdb=" SG CYS A 142 " pdb=" CB CYS A 142 " ideal model delta sinusoidal sigma weight residual -86.00 -12.06 -73.94 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS D 110 " pdb=" SG CYS D 110 " pdb=" SG CYS D 142 " pdb=" CB CYS D 142 " ideal model delta sinusoidal sigma weight residual -86.00 -12.07 -73.93 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS C 110 " pdb=" SG CYS C 110 " pdb=" SG CYS C 142 " pdb=" CB CYS C 142 " ideal model delta sinusoidal sigma weight residual -86.00 -12.08 -73.92 1 1.00e+01 1.00e-02 6.94e+01 ... (remaining 6125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 834 0.029 - 0.058: 487 0.058 - 0.086: 148 0.086 - 0.115: 145 0.115 - 0.144: 38 Chirality restraints: 1652 Sorted by residual: chirality pdb=" CB ILE B 210 " pdb=" CA ILE B 210 " pdb=" CG1 ILE B 210 " pdb=" CG2 ILE B 210 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CB ILE A 210 " pdb=" CA ILE A 210 " pdb=" CG1 ILE A 210 " pdb=" CG2 ILE A 210 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CB ILE D 210 " pdb=" CA ILE D 210 " pdb=" CG1 ILE D 210 " pdb=" CG2 ILE D 210 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 1649 not shown) Planarity restraints: 1764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP D 68 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO D 69 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 69 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 69 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 68 " -0.026 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO B 69 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 69 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 69 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP C 68 " -0.026 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO C 69 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 69 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 69 " -0.022 5.00e-02 4.00e+02 ... (remaining 1761 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 3141 2.83 - 3.41: 10274 3.41 - 3.98: 19076 3.98 - 4.56: 26741 4.56 - 5.14: 40974 Nonbonded interactions: 100206 Sorted by model distance: nonbonded pdb=" O PRO C 109 " pdb=" OG1 THR C 139 " model vdw 2.252 2.440 nonbonded pdb=" O PRO B 109 " pdb=" OG1 THR B 139 " model vdw 2.252 2.440 nonbonded pdb=" O PRO D 109 " pdb=" OG1 THR D 139 " model vdw 2.252 2.440 nonbonded pdb=" O PRO A 109 " pdb=" OG1 THR A 139 " model vdw 2.253 2.440 nonbonded pdb=" OE2 GLU C 140 " pdb=" OG SER D 119 " model vdw 2.263 2.440 ... (remaining 100201 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 32 through 352) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.550 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.570 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 : 0.005 0.043 10304 Z= 0.335 Angle : 0.677 6.459 14008 Z= 0.398 Chirality : 0.048 0.144 1652 Planarity : 0.005 0.039 1764 Dihedral : 15.459 84.882 3700 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.68 % Allowed : 16.19 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.19), residues: 1276 helix: -1.26 (0.21), residues: 396 sheet: -1.35 (0.31), residues: 256 loop : -1.87 (0.20), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 311 HIS 0.003 0.001 HIS D 175 PHE 0.015 0.002 PHE B 75 TYR 0.007 0.001 TYR A 258 ARG 0.002 0.000 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 172 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8968 (mmtm) cc_final: 0.8742 (mtmm) REVERT: A 47 LYS cc_start: 0.8461 (mtpp) cc_final: 0.8228 (mtpp) REVERT: A 332 LYS cc_start: 0.9210 (mttt) cc_final: 0.8944 (mtpp) REVERT: B 110 CYS cc_start: 0.6924 (OUTLIER) cc_final: 0.6448 (m) REVERT: B 137 MET cc_start: 0.9032 (ptt) cc_final: 0.8364 (ptm) REVERT: B 169 MET cc_start: 0.8866 (ttm) cc_final: 0.8451 (ttm) REVERT: B 185 LYS cc_start: 0.8927 (ttpp) cc_final: 0.8659 (ttpt) REVERT: B 222 LYS cc_start: 0.9133 (ttmt) cc_final: 0.8628 (ttpp) REVERT: B 225 SER cc_start: 0.8256 (OUTLIER) cc_final: 0.7555 (p) REVERT: C 67 LYS cc_start: 0.7945 (mttp) cc_final: 0.7208 (mmmt) REVERT: C 88 MET cc_start: 0.7668 (mtt) cc_final: 0.7462 (mtt) REVERT: C 102 PRO cc_start: 0.7896 (Cg_endo) cc_final: 0.7666 (Cg_exo) REVERT: C 185 LYS cc_start: 0.8762 (ttpp) cc_final: 0.8477 (tptt) REVERT: C 240 MET cc_start: 0.9007 (ttp) cc_final: 0.8788 (ttp) REVERT: C 304 TYR cc_start: 0.9174 (m-80) cc_final: 0.8871 (m-80) REVERT: D 47 LYS cc_start: 0.8207 (mtpp) cc_final: 0.7880 (mmtt) REVERT: D 67 LYS cc_start: 0.7763 (mttp) cc_final: 0.7460 (mtmt) REVERT: D 102 PRO cc_start: 0.7467 (Cg_endo) cc_final: 0.7149 (Cg_exo) REVERT: D 199 MET cc_start: 0.9054 (mtm) cc_final: 0.8827 (mtp) REVERT: D 217 MET cc_start: 0.8874 (mtm) cc_final: 0.8635 (mtm) outliers start: 52 outliers final: 27 residues processed: 215 average time/residue: 0.2348 time to fit residues: 69.1150 Evaluate side-chains 161 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 110 CYS Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 337 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 0.0870 chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 0.0270 chunk 65 optimal weight: 0.9980 chunk 51 optimal weight: 0.0980 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.0470 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.2114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 160 ASN A 218 GLN A 235 GLN A 276 HIS A 277 HIS B 48 ASN B 218 GLN B 235 GLN B 276 HIS B 277 HIS B 348 GLN C 41 ASN C 218 GLN C 235 GLN C 276 HIS C 348 GLN D 48 ASN D 218 GLN D 235 GLN D 264 ASN D 276 HIS D 277 HIS D 348 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10304 Z= 0.123 Angle : 0.452 7.372 14008 Z= 0.243 Chirality : 0.043 0.127 1652 Planarity : 0.003 0.027 1764 Dihedral : 6.136 75.719 1403 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.69 % Allowed : 15.56 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.22), residues: 1276 helix: 0.72 (0.26), residues: 400 sheet: -0.37 (0.35), residues: 216 loop : -1.04 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 68 HIS 0.002 0.000 HIS B 276 PHE 0.014 0.001 PHE B 75 TYR 0.007 0.001 TYR C 258 ARG 0.001 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 146 time to evaluate : 1.936 Fit side-chains REVERT: A 39 LYS cc_start: 0.8987 (mmtm) cc_final: 0.8771 (mtmm) REVERT: A 67 LYS cc_start: 0.7975 (mttp) cc_final: 0.7383 (mmmt) REVERT: A 77 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7848 (mpp) REVERT: A 247 ASN cc_start: 0.8344 (p0) cc_final: 0.8041 (p0) REVERT: A 258 TYR cc_start: 0.8916 (p90) cc_final: 0.8332 (p90) REVERT: A 268 TYR cc_start: 0.9139 (t80) cc_final: 0.8716 (t80) REVERT: A 330 TYR cc_start: 0.8845 (m-80) cc_final: 0.8544 (m-10) REVERT: A 331 SER cc_start: 0.9169 (OUTLIER) cc_final: 0.8954 (m) REVERT: B 47 LYS cc_start: 0.8190 (mtpp) cc_final: 0.7660 (mmmt) REVERT: B 137 MET cc_start: 0.8942 (ptt) cc_final: 0.8240 (ptm) REVERT: B 169 MET cc_start: 0.8660 (ttm) cc_final: 0.8405 (ttm) REVERT: B 185 LYS cc_start: 0.8943 (ttpp) cc_final: 0.8570 (ttpt) REVERT: B 222 LYS cc_start: 0.9183 (ttmt) cc_final: 0.8869 (ttpp) REVERT: B 235 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8814 (mt0) REVERT: B 258 TYR cc_start: 0.8947 (p90) cc_final: 0.8625 (p90) REVERT: B 277 HIS cc_start: 0.7452 (OUTLIER) cc_final: 0.7113 (t70) REVERT: C 67 LYS cc_start: 0.8034 (mttp) cc_final: 0.7357 (mmmt) REVERT: C 185 LYS cc_start: 0.8766 (ttpp) cc_final: 0.8453 (tptt) REVERT: C 207 LYS cc_start: 0.8938 (tptm) cc_final: 0.8678 (tptt) REVERT: C 304 TYR cc_start: 0.9106 (m-80) cc_final: 0.8801 (m-80) REVERT: C 334 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8362 (m-30) REVERT: D 47 LYS cc_start: 0.8109 (mtpp) cc_final: 0.7871 (mmtm) REVERT: D 67 LYS cc_start: 0.7893 (mttp) cc_final: 0.7539 (mtmt) REVERT: D 93 ILE cc_start: 0.9272 (mm) cc_final: 0.9056 (mt) REVERT: D 217 MET cc_start: 0.8789 (mtm) cc_final: 0.8583 (mtm) REVERT: D 280 ASP cc_start: 0.8024 (t0) cc_final: 0.7642 (t70) REVERT: D 338 LYS cc_start: 0.8340 (mtpp) cc_final: 0.7666 (tptt) outliers start: 41 outliers final: 17 residues processed: 182 average time/residue: 0.2621 time to fit residues: 65.5199 Evaluate side-chains 155 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 277 HIS Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 334 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 116 optimal weight: 0.0470 chunk 125 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 235 GLN B 160 ASN B 235 GLN B 277 HIS C 41 ASN C 235 GLN D 235 GLN D 277 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10304 Z= 0.181 Angle : 0.451 5.964 14008 Z= 0.242 Chirality : 0.043 0.129 1652 Planarity : 0.003 0.027 1764 Dihedral : 4.952 39.852 1378 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.24 % Allowed : 16.73 % Favored : 80.04 % 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: -0.14 (0.23), residues: 1276 helix: 1.52 (0.27), residues: 400 sheet: -0.81 (0.31), residues: 252 loop : -0.82 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 68 HIS 0.003 0.001 HIS A 277 PHE 0.014 0.001 PHE C 75 TYR 0.009 0.001 TYR C 330 ARG 0.001 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 137 time to evaluate : 1.166 Fit side-chains REVERT: A 39 LYS cc_start: 0.9007 (mmtm) cc_final: 0.8799 (mtmm) REVERT: A 67 LYS cc_start: 0.7993 (mttp) cc_final: 0.7394 (mmmt) REVERT: A 77 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7833 (mpp) REVERT: A 160 ASN cc_start: 0.8378 (m-40) cc_final: 0.7810 (m110) REVERT: A 268 TYR cc_start: 0.9137 (t80) cc_final: 0.8781 (t80) REVERT: A 330 TYR cc_start: 0.8955 (m-80) cc_final: 0.8746 (m-80) REVERT: B 47 LYS cc_start: 0.8116 (mtpp) cc_final: 0.7610 (mmmt) REVERT: B 50 ARG cc_start: 0.6626 (mmt-90) cc_final: 0.6380 (mmp80) REVERT: B 65 ASP cc_start: 0.8153 (m-30) cc_final: 0.7925 (m-30) REVERT: B 137 MET cc_start: 0.9039 (ptt) cc_final: 0.8345 (ptm) REVERT: B 160 ASN cc_start: 0.8399 (m-40) cc_final: 0.8103 (m110) REVERT: B 169 MET cc_start: 0.8698 (ttm) cc_final: 0.8398 (ttm) REVERT: B 185 LYS cc_start: 0.8893 (ttpp) cc_final: 0.8544 (ttpt) REVERT: B 235 GLN cc_start: 0.9098 (OUTLIER) cc_final: 0.8714 (mt0) REVERT: B 258 TYR cc_start: 0.8907 (p90) cc_final: 0.8499 (p90) REVERT: C 67 LYS cc_start: 0.8050 (mttp) cc_final: 0.7368 (mmmt) REVERT: C 185 LYS cc_start: 0.8790 (ttpp) cc_final: 0.8469 (tptt) REVERT: C 207 LYS cc_start: 0.8910 (tptm) cc_final: 0.8601 (tptt) REVERT: C 334 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8316 (m-30) REVERT: D 32 ARG cc_start: 0.6348 (mmt90) cc_final: 0.5956 (mmt90) REVERT: D 47 LYS cc_start: 0.8114 (mtpp) cc_final: 0.7751 (mmtm) REVERT: D 67 LYS cc_start: 0.7884 (mttp) cc_final: 0.7476 (mtmt) REVERT: D 278 HIS cc_start: 0.7486 (OUTLIER) cc_final: 0.6847 (m-70) REVERT: D 305 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8615 (mm) REVERT: D 338 LYS cc_start: 0.8348 (mtpp) cc_final: 0.7664 (tptt) outliers start: 36 outliers final: 21 residues processed: 167 average time/residue: 0.2636 time to fit residues: 59.1130 Evaluate side-chains 160 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 277 HIS Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 334 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 0.0670 chunk 78 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 61 optimal weight: 0.4980 chunk 110 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.1120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN A 277 HIS B 235 GLN B 277 HIS C 41 ASN C 235 GLN D 235 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10304 Z= 0.309 Angle : 0.489 5.317 14008 Z= 0.262 Chirality : 0.045 0.197 1652 Planarity : 0.003 0.028 1764 Dihedral : 4.977 41.876 1378 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.15 % Allowed : 17.54 % Favored : 79.32 % 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: 0.06 (0.24), residues: 1276 helix: 1.68 (0.27), residues: 400 sheet: -0.85 (0.31), residues: 256 loop : -0.60 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 311 HIS 0.006 0.001 HIS D 277 PHE 0.015 0.002 PHE C 75 TYR 0.009 0.001 TYR A 258 ARG 0.001 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 144 time to evaluate : 1.233 Fit side-chains REVERT: A 67 LYS cc_start: 0.7998 (mttp) cc_final: 0.7389 (mmmt) REVERT: A 77 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7839 (mpp) REVERT: A 268 TYR cc_start: 0.9132 (t80) cc_final: 0.8774 (t80) REVERT: A 338 LYS cc_start: 0.8878 (mtpp) cc_final: 0.8636 (mtpp) REVERT: B 47 LYS cc_start: 0.8174 (mtpp) cc_final: 0.7774 (mmmt) REVERT: B 50 ARG cc_start: 0.6697 (mmt-90) cc_final: 0.6433 (mmp80) REVERT: B 65 ASP cc_start: 0.8266 (m-30) cc_final: 0.8011 (m-30) REVERT: B 67 LYS cc_start: 0.7986 (mttp) cc_final: 0.7631 (mtpt) REVERT: B 77 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7561 (mpp) REVERT: B 137 MET cc_start: 0.9100 (ptt) cc_final: 0.8397 (ptm) REVERT: B 169 MET cc_start: 0.8730 (ttm) cc_final: 0.8400 (ttm) REVERT: B 185 LYS cc_start: 0.8880 (ttpp) cc_final: 0.8506 (ttpt) REVERT: B 222 LYS cc_start: 0.9234 (ttmm) cc_final: 0.8810 (ttpp) REVERT: B 258 TYR cc_start: 0.8897 (p90) cc_final: 0.8444 (p90) REVERT: C 67 LYS cc_start: 0.8085 (mttp) cc_final: 0.7382 (mmmt) REVERT: C 185 LYS cc_start: 0.8842 (ttpp) cc_final: 0.8429 (tptt) REVERT: C 207 LYS cc_start: 0.8900 (tptm) cc_final: 0.8623 (tptt) REVERT: C 235 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8779 (mt0) REVERT: C 255 LEU cc_start: 0.8951 (pp) cc_final: 0.8632 (pp) REVERT: C 334 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8330 (m-30) REVERT: D 47 LYS cc_start: 0.8206 (mtpp) cc_final: 0.7937 (mmtm) REVERT: D 67 LYS cc_start: 0.7917 (mttp) cc_final: 0.7509 (mtmt) REVERT: D 278 HIS cc_start: 0.7609 (OUTLIER) cc_final: 0.7130 (m-70) REVERT: D 305 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8555 (mm) REVERT: D 338 LYS cc_start: 0.8362 (mtpp) cc_final: 0.7755 (tptt) outliers start: 35 outliers final: 20 residues processed: 169 average time/residue: 0.2866 time to fit residues: 64.4423 Evaluate side-chains 166 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 334 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 0.0470 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 235 GLN B 277 HIS C 41 ASN C 235 GLN D 235 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10304 Z= 0.247 Angle : 0.464 5.270 14008 Z= 0.249 Chirality : 0.044 0.166 1652 Planarity : 0.003 0.030 1764 Dihedral : 4.836 41.536 1377 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.51 % Allowed : 17.18 % Favored : 79.32 % 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: 0.35 (0.24), residues: 1276 helix: 1.79 (0.27), residues: 400 sheet: -0.49 (0.32), residues: 240 loop : -0.44 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 311 HIS 0.004 0.001 HIS A 277 PHE 0.014 0.001 PHE C 75 TYR 0.008 0.001 TYR A 258 ARG 0.001 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 146 time to evaluate : 3.276 Fit side-chains REVERT: A 67 LYS cc_start: 0.8077 (mttp) cc_final: 0.7509 (mmmt) REVERT: A 77 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7837 (mpp) REVERT: A 160 ASN cc_start: 0.8415 (m-40) cc_final: 0.7893 (m110) REVERT: A 268 TYR cc_start: 0.9118 (t80) cc_final: 0.8785 (t80) REVERT: B 47 LYS cc_start: 0.8159 (mtpp) cc_final: 0.7737 (mmmt) REVERT: B 65 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.8010 (m-30) REVERT: B 67 LYS cc_start: 0.7912 (mttp) cc_final: 0.7568 (mtpt) REVERT: B 77 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7583 (mpp) REVERT: B 137 MET cc_start: 0.9063 (ptt) cc_final: 0.8615 (ptm) REVERT: B 169 MET cc_start: 0.8677 (ttm) cc_final: 0.8346 (ttm) REVERT: B 185 LYS cc_start: 0.8877 (ttpp) cc_final: 0.8494 (ttpt) REVERT: B 222 LYS cc_start: 0.9232 (ttmm) cc_final: 0.8804 (ttpp) REVERT: B 258 TYR cc_start: 0.8869 (p90) cc_final: 0.8398 (p90) REVERT: C 67 LYS cc_start: 0.8090 (mttp) cc_final: 0.7385 (mmmt) REVERT: C 185 LYS cc_start: 0.8834 (ttpp) cc_final: 0.8459 (tptt) REVERT: C 207 LYS cc_start: 0.8923 (tptm) cc_final: 0.8711 (tptt) REVERT: C 235 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8783 (mt0) REVERT: C 334 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8286 (m-30) REVERT: D 47 LYS cc_start: 0.8199 (mtpp) cc_final: 0.7885 (mttm) REVERT: D 67 LYS cc_start: 0.7927 (mttp) cc_final: 0.7518 (mtmt) REVERT: D 278 HIS cc_start: 0.7505 (OUTLIER) cc_final: 0.7050 (m-70) REVERT: D 305 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8577 (mm) REVERT: D 338 LYS cc_start: 0.8459 (mtpp) cc_final: 0.7749 (tptt) outliers start: 39 outliers final: 20 residues processed: 172 average time/residue: 0.3216 time to fit residues: 73.4675 Evaluate side-chains 169 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 142 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 305 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 0.0980 chunk 57 optimal weight: 3.9990 chunk 10 optimal weight: 0.3980 chunk 40 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN B 277 HIS C 41 ASN C 235 GLN D 235 GLN D 277 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10304 Z= 0.188 Angle : 0.444 5.226 14008 Z= 0.239 Chirality : 0.043 0.145 1652 Planarity : 0.003 0.030 1764 Dihedral : 4.568 41.719 1373 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.88 % Allowed : 18.08 % Favored : 79.05 % 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: 0.55 (0.24), residues: 1276 helix: 1.89 (0.27), residues: 400 sheet: -0.16 (0.35), residues: 220 loop : -0.36 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 68 HIS 0.003 0.000 HIS A 277 PHE 0.014 0.001 PHE D 75 TYR 0.018 0.001 TYR C 268 ARG 0.001 0.000 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 149 time to evaluate : 1.213 Fit side-chains REVERT: A 67 LYS cc_start: 0.8075 (mttp) cc_final: 0.7510 (mmmt) REVERT: A 77 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7856 (mpp) REVERT: A 268 TYR cc_start: 0.9103 (t80) cc_final: 0.8816 (t80) REVERT: B 47 LYS cc_start: 0.8128 (mtpp) cc_final: 0.7730 (mmmt) REVERT: B 67 LYS cc_start: 0.7911 (mttp) cc_final: 0.7567 (mtpt) REVERT: B 77 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7485 (mpp) REVERT: B 137 MET cc_start: 0.9051 (ptt) cc_final: 0.8619 (ptm) REVERT: B 169 MET cc_start: 0.8637 (ttm) cc_final: 0.8312 (ttm) REVERT: B 185 LYS cc_start: 0.8924 (ttpp) cc_final: 0.8529 (ttpt) REVERT: B 258 TYR cc_start: 0.8818 (p90) cc_final: 0.8204 (p90) REVERT: C 67 LYS cc_start: 0.8087 (mttp) cc_final: 0.7392 (mmmt) REVERT: C 185 LYS cc_start: 0.8818 (ttpp) cc_final: 0.8423 (tptt) REVERT: C 207 LYS cc_start: 0.8929 (tptm) cc_final: 0.8589 (tptt) REVERT: C 334 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8127 (m-30) REVERT: D 47 LYS cc_start: 0.8196 (mtpp) cc_final: 0.7862 (mttm) REVERT: D 67 LYS cc_start: 0.7875 (mttp) cc_final: 0.7159 (tptt) REVERT: D 278 HIS cc_start: 0.7475 (OUTLIER) cc_final: 0.7069 (m-70) REVERT: D 305 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8607 (mm) REVERT: D 338 LYS cc_start: 0.8463 (mtpp) cc_final: 0.7751 (tptt) outliers start: 32 outliers final: 19 residues processed: 170 average time/residue: 0.2667 time to fit residues: 60.7398 Evaluate side-chains 168 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 305 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 56 optimal weight: 0.0070 chunk 76 optimal weight: 0.6980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 235 GLN B 277 HIS C 41 ASN C 235 GLN D 235 GLN D 277 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10304 Z= 0.202 Angle : 0.443 5.233 14008 Z= 0.239 Chirality : 0.043 0.135 1652 Planarity : 0.003 0.036 1764 Dihedral : 4.492 42.125 1372 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.06 % Allowed : 18.35 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.24), residues: 1276 helix: 1.94 (0.27), residues: 400 sheet: -0.13 (0.35), residues: 220 loop : -0.28 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 311 HIS 0.003 0.001 HIS D 276 PHE 0.014 0.001 PHE D 75 TYR 0.012 0.001 TYR C 268 ARG 0.001 0.000 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 150 time to evaluate : 1.242 Fit side-chains REVERT: A 67 LYS cc_start: 0.8074 (mttp) cc_final: 0.7511 (mmmt) REVERT: A 77 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7855 (mpp) REVERT: A 160 ASN cc_start: 0.8362 (m-40) cc_final: 0.7849 (m110) REVERT: A 268 TYR cc_start: 0.9101 (t80) cc_final: 0.8814 (t80) REVERT: A 332 LYS cc_start: 0.9251 (mtpt) cc_final: 0.9045 (mtpp) REVERT: B 47 LYS cc_start: 0.8136 (mtpp) cc_final: 0.7753 (mmmt) REVERT: B 67 LYS cc_start: 0.7933 (mttp) cc_final: 0.7589 (mtpt) REVERT: B 77 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7490 (mpp) REVERT: B 137 MET cc_start: 0.8971 (ptt) cc_final: 0.8558 (ptm) REVERT: B 169 MET cc_start: 0.8640 (ttm) cc_final: 0.8312 (ttm) REVERT: B 185 LYS cc_start: 0.8921 (ttpp) cc_final: 0.8521 (ttpt) REVERT: B 258 TYR cc_start: 0.8744 (p90) cc_final: 0.8186 (p90) REVERT: C 67 LYS cc_start: 0.8080 (mttp) cc_final: 0.7389 (mmmt) REVERT: C 185 LYS cc_start: 0.8809 (ttpp) cc_final: 0.8462 (tptt) REVERT: C 207 LYS cc_start: 0.8925 (tptm) cc_final: 0.8618 (tptt) REVERT: C 334 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8170 (m-30) REVERT: D 47 LYS cc_start: 0.8195 (mtpp) cc_final: 0.7875 (mmtm) REVERT: D 67 LYS cc_start: 0.7856 (mttp) cc_final: 0.7150 (tptt) REVERT: D 278 HIS cc_start: 0.7488 (OUTLIER) cc_final: 0.7078 (m-70) REVERT: D 305 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8600 (mm) REVERT: D 338 LYS cc_start: 0.8493 (mtpp) cc_final: 0.7767 (tptt) outliers start: 34 outliers final: 21 residues processed: 173 average time/residue: 0.2638 time to fit residues: 61.4051 Evaluate side-chains 172 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 334 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN B 277 HIS C 41 ASN C 235 GLN D 235 GLN D 277 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10304 Z= 0.275 Angle : 0.472 5.278 14008 Z= 0.253 Chirality : 0.044 0.134 1652 Planarity : 0.003 0.030 1764 Dihedral : 4.574 42.973 1372 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.06 % Allowed : 18.35 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.24), residues: 1276 helix: 1.89 (0.27), residues: 400 sheet: -0.28 (0.33), residues: 236 loop : -0.29 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 311 HIS 0.003 0.001 HIS D 276 PHE 0.015 0.001 PHE C 75 TYR 0.011 0.002 TYR C 330 ARG 0.001 0.000 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 1.121 Fit side-chains REVERT: A 77 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7843 (mpp) REVERT: A 268 TYR cc_start: 0.9112 (t80) cc_final: 0.8793 (t80) REVERT: A 332 LYS cc_start: 0.9255 (mtpt) cc_final: 0.9053 (mtpp) REVERT: B 47 LYS cc_start: 0.8147 (mtpp) cc_final: 0.7743 (mmmt) REVERT: B 67 LYS cc_start: 0.7962 (mttp) cc_final: 0.7692 (mtpt) REVERT: B 77 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7521 (mpp) REVERT: B 137 MET cc_start: 0.8966 (ptt) cc_final: 0.8538 (ptm) REVERT: B 160 ASN cc_start: 0.8365 (m-40) cc_final: 0.8142 (m-40) REVERT: B 169 MET cc_start: 0.8667 (ttm) cc_final: 0.8331 (ttm) REVERT: B 185 LYS cc_start: 0.8920 (ttpp) cc_final: 0.8517 (ttpt) REVERT: B 222 LYS cc_start: 0.9204 (ttmm) cc_final: 0.8751 (ttpp) REVERT: C 67 LYS cc_start: 0.8072 (mttp) cc_final: 0.7386 (mmmt) REVERT: C 185 LYS cc_start: 0.8805 (ttpp) cc_final: 0.8381 (tptt) REVERT: C 207 LYS cc_start: 0.8939 (tptm) cc_final: 0.8611 (tptt) REVERT: C 217 MET cc_start: 0.8840 (mtp) cc_final: 0.8626 (mtm) REVERT: C 334 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8168 (m-30) REVERT: D 47 LYS cc_start: 0.8197 (mtpp) cc_final: 0.7859 (mmtm) REVERT: D 67 LYS cc_start: 0.7842 (mttp) cc_final: 0.7133 (tptt) REVERT: D 278 HIS cc_start: 0.7505 (OUTLIER) cc_final: 0.7092 (m-70) REVERT: D 305 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8566 (mm) REVERT: D 338 LYS cc_start: 0.8509 (mtpp) cc_final: 0.7774 (tptt) outliers start: 34 outliers final: 22 residues processed: 169 average time/residue: 0.2671 time to fit residues: 60.5277 Evaluate side-chains 171 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 144 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 305 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 0.2980 chunk 107 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 103 optimal weight: 0.4980 chunk 108 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 235 GLN B 277 HIS C 41 ASN C 235 GLN D 235 GLN D 277 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10304 Z= 0.171 Angle : 0.440 5.215 14008 Z= 0.236 Chirality : 0.043 0.131 1652 Planarity : 0.003 0.031 1764 Dihedral : 4.449 43.216 1372 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.97 % Allowed : 18.35 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.24), residues: 1276 helix: 1.98 (0.27), residues: 400 sheet: 0.06 (0.35), residues: 216 loop : -0.26 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 68 HIS 0.003 0.000 HIS D 276 PHE 0.014 0.001 PHE D 75 TYR 0.009 0.001 TYR C 330 ARG 0.001 0.000 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 146 time to evaluate : 1.306 Fit side-chains REVERT: A 77 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7836 (mpp) REVERT: A 160 ASN cc_start: 0.8346 (m-40) cc_final: 0.7867 (m110) REVERT: A 268 TYR cc_start: 0.9093 (t80) cc_final: 0.8746 (t80) REVERT: A 332 LYS cc_start: 0.9245 (mtpt) cc_final: 0.9034 (mtpp) REVERT: B 67 LYS cc_start: 0.8055 (mttp) cc_final: 0.7819 (mtpt) REVERT: B 77 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7506 (mpp) REVERT: B 137 MET cc_start: 0.8971 (ptt) cc_final: 0.8541 (ptm) REVERT: B 160 ASN cc_start: 0.8299 (m-40) cc_final: 0.8043 (m-40) REVERT: B 169 MET cc_start: 0.8621 (ttm) cc_final: 0.8307 (ttm) REVERT: B 185 LYS cc_start: 0.8923 (ttpp) cc_final: 0.8522 (ttpt) REVERT: B 258 TYR cc_start: 0.8706 (p90) cc_final: 0.8181 (p90) REVERT: C 67 LYS cc_start: 0.8069 (mttp) cc_final: 0.7261 (tptp) REVERT: C 185 LYS cc_start: 0.8808 (ttpp) cc_final: 0.8395 (tptt) REVERT: C 207 LYS cc_start: 0.8915 (tptm) cc_final: 0.8573 (tptt) REVERT: C 217 MET cc_start: 0.8764 (mtp) cc_final: 0.8547 (mtm) REVERT: D 47 LYS cc_start: 0.8173 (mtpp) cc_final: 0.7819 (mmtm) REVERT: D 67 LYS cc_start: 0.7837 (mttp) cc_final: 0.7128 (tptt) REVERT: D 278 HIS cc_start: 0.7488 (OUTLIER) cc_final: 0.7085 (m-70) REVERT: D 305 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8595 (mm) REVERT: D 338 LYS cc_start: 0.8488 (mtpp) cc_final: 0.7765 (tptt) outliers start: 33 outliers final: 25 residues processed: 171 average time/residue: 0.2712 time to fit residues: 61.9431 Evaluate side-chains 173 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 144 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 334 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 chunk 127 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 10 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 0.0870 chunk 80 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN B 277 HIS C 41 ASN C 235 GLN D 235 GLN D 277 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10304 Z= 0.151 Angle : 0.435 5.202 14008 Z= 0.234 Chirality : 0.043 0.132 1652 Planarity : 0.003 0.031 1764 Dihedral : 4.303 43.109 1370 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.79 % Allowed : 18.53 % Favored : 78.69 % 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: 0.81 (0.24), residues: 1276 helix: 2.03 (0.27), residues: 400 sheet: 0.11 (0.35), residues: 216 loop : -0.20 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 68 HIS 0.003 0.000 HIS D 276 PHE 0.014 0.001 PHE D 75 TYR 0.009 0.001 TYR C 330 ARG 0.001 0.000 ARG A 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 151 time to evaluate : 1.122 Fit side-chains REVERT: A 77 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7827 (mpp) REVERT: A 160 ASN cc_start: 0.8226 (m-40) cc_final: 0.7697 (m110) REVERT: A 204 ASP cc_start: 0.7446 (t70) cc_final: 0.6580 (p0) REVERT: A 268 TYR cc_start: 0.9086 (t80) cc_final: 0.8763 (t80) REVERT: A 332 LYS cc_start: 0.9243 (mtpt) cc_final: 0.8998 (mtpp) REVERT: B 67 LYS cc_start: 0.7885 (mttp) cc_final: 0.7598 (mtpt) REVERT: B 77 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7411 (mpp) REVERT: B 137 MET cc_start: 0.8952 (ptt) cc_final: 0.8564 (ptm) REVERT: B 160 ASN cc_start: 0.8334 (m-40) cc_final: 0.8065 (m-40) REVERT: B 169 MET cc_start: 0.8595 (ttm) cc_final: 0.8280 (ttm) REVERT: B 185 LYS cc_start: 0.8920 (ttpp) cc_final: 0.8525 (ttpt) REVERT: B 258 TYR cc_start: 0.8639 (p90) cc_final: 0.8156 (p90) REVERT: C 67 LYS cc_start: 0.8092 (mttp) cc_final: 0.7342 (tptp) REVERT: C 185 LYS cc_start: 0.8800 (ttpp) cc_final: 0.8510 (tptt) REVERT: C 207 LYS cc_start: 0.8916 (tptm) cc_final: 0.8563 (tptt) REVERT: C 209 MET cc_start: 0.8700 (tpp) cc_final: 0.8486 (tpp) REVERT: C 217 MET cc_start: 0.8777 (mtp) cc_final: 0.8574 (mtm) REVERT: D 47 LYS cc_start: 0.8188 (mtpp) cc_final: 0.7777 (mtpp) REVERT: D 67 LYS cc_start: 0.7903 (mttp) cc_final: 0.7148 (tptt) REVERT: D 278 HIS cc_start: 0.7466 (OUTLIER) cc_final: 0.7072 (m-70) REVERT: D 305 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8585 (mm) REVERT: D 338 LYS cc_start: 0.8470 (mtpp) cc_final: 0.7756 (tptt) outliers start: 31 outliers final: 23 residues processed: 174 average time/residue: 0.2620 time to fit residues: 62.0065 Evaluate side-chains 175 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 305 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 104 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN B 277 HIS C 41 ASN C 235 GLN D 216 HIS D 235 GLN D 277 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.091929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.082182 restraints weight = 16101.560| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.84 r_work: 0.2862 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10304 Z= 0.264 Angle : 0.468 5.273 14008 Z= 0.251 Chirality : 0.044 0.131 1652 Planarity : 0.003 0.030 1764 Dihedral : 4.409 43.644 1370 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.79 % Allowed : 18.71 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.24), residues: 1276 helix: 1.94 (0.27), residues: 400 sheet: -0.29 (0.34), residues: 232 loop : -0.25 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 311 HIS 0.003 0.001 HIS D 216 PHE 0.014 0.001 PHE C 75 TYR 0.010 0.001 TYR C 330 ARG 0.003 0.000 ARG A 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2517.97 seconds wall clock time: 46 minutes 17.39 seconds (2777.39 seconds total)