Starting phenix.real_space_refine on Thu Mar 14 23:11:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g17_29664/03_2024/8g17_29664.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g17_29664/03_2024/8g17_29664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g17_29664/03_2024/8g17_29664.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g17_29664/03_2024/8g17_29664.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g17_29664/03_2024/8g17_29664.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g17_29664/03_2024/8g17_29664.pdb" } resolution = 1.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 48 5.16 5 C 6328 2.51 5 N 1744 2.21 5 O 1896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10016 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2504 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2504 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2504 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2504 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 5.30, per 1000 atoms: 0.53 Number of scatterers: 10016 At special positions: 0 Unit cell: (99.365, 101.035, 91.015, 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 48 16.00 O 1896 8.00 N 1744 7.00 C 6328 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: 3.72 Conformation dependent library (CDL) restraints added in 1.8 seconds 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 12 sheets defined 39.2% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 12 through 26 Processing helix chain 'A' and resid 39 through 49 Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 109 through 114 removed outlier: 3.918A pdb=" N GLN A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 109 through 114' Processing helix chain 'A' and resid 136 through 140 Processing helix chain 'A' and resid 151 through 169 Proline residue: A 159 - end of helix Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 212 through 221 removed outlier: 3.816A pdb=" N GLY A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 254 through 268 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 317 through 334 Processing helix chain 'B' and resid 12 through 26 Processing helix chain 'B' and resid 39 through 49 Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 109 through 114 removed outlier: 3.918A pdb=" N GLN B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 109 through 114' Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 151 through 169 Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 212 through 221 removed outlier: 3.816A pdb=" N GLY B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 254 through 268 Processing helix chain 'B' and resid 282 through 287 Processing helix chain 'B' and resid 317 through 334 Processing helix chain 'C' and resid 12 through 26 Processing helix chain 'C' and resid 39 through 49 Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 109 through 114 removed outlier: 3.919A pdb=" N GLN C 113 " --> pdb=" O GLY C 109 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 109 through 114' Processing helix chain 'C' and resid 136 through 140 Processing helix chain 'C' and resid 151 through 169 Proline residue: C 159 - end of helix Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 212 through 221 removed outlier: 3.816A pdb=" N GLY C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS C 219 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 254 through 268 Processing helix chain 'C' and resid 282 through 287 Processing helix chain 'C' and resid 317 through 334 Processing helix chain 'D' and resid 12 through 26 Processing helix chain 'D' and resid 39 through 49 Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 109 through 114 removed outlier: 3.918A pdb=" N GLN D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 109 through 114' Processing helix chain 'D' and resid 136 through 140 Processing helix chain 'D' and resid 151 through 169 Proline residue: D 159 - end of helix Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 212 through 221 removed outlier: 3.816A pdb=" N GLY D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS D 219 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 282 through 287 Processing helix chain 'D' and resid 317 through 334 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63 removed outlier: 10.277A pdb=" N ASP A 29 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 9.816A pdb=" N THR A 75 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A 31 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N PHE A 77 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE A 33 " --> pdb=" O PHE A 77 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL A 8 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE A 33 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL A 95 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 210 removed outlier: 3.604A pdb=" N THR A 229 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG A 248 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY A 173 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR A 246 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N MET A 175 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASP A 244 " --> pdb=" O MET A 175 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N THR A 177 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL A 242 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ILE A 311 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 210 removed outlier: 3.604A pdb=" N THR A 229 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG A 248 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY A 173 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR A 246 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N MET A 175 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASP A 244 " --> pdb=" O MET A 175 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N THR A 177 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL A 242 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N PHE A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 63 removed outlier: 10.277A pdb=" N ASP B 29 " --> pdb=" O PRO B 73 " (cutoff:3.500A) removed outlier: 9.815A pdb=" N THR B 75 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B 31 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N PHE B 77 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE B 33 " --> pdb=" O PHE B 77 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL B 8 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE B 33 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL B 95 " --> pdb=" O ILE B 120 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 208 through 210 removed outlier: 3.604A pdb=" N THR B 229 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG B 248 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY B 173 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR B 246 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N MET B 175 " --> pdb=" O ASP B 244 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP B 244 " --> pdb=" O MET B 175 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N THR B 177 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B 242 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ILE B 311 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 208 through 210 removed outlier: 3.604A pdb=" N THR B 229 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG B 248 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY B 173 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR B 246 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N MET B 175 " --> pdb=" O ASP B 244 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP B 244 " --> pdb=" O MET B 175 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N THR B 177 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B 242 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N PHE B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 63 removed outlier: 10.277A pdb=" N ASP C 29 " --> pdb=" O PRO C 73 " (cutoff:3.500A) removed outlier: 9.815A pdb=" N THR C 75 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C 31 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N PHE C 77 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE C 33 " --> pdb=" O PHE C 77 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL C 8 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE C 33 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL C 95 " --> pdb=" O ILE C 120 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 208 through 210 removed outlier: 3.605A pdb=" N THR C 229 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG C 248 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY C 173 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR C 246 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N MET C 175 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP C 244 " --> pdb=" O MET C 175 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N THR C 177 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL C 242 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ILE C 311 " --> pdb=" O ASP C 296 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 208 through 210 removed outlier: 3.605A pdb=" N THR C 229 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG C 248 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY C 173 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR C 246 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N MET C 175 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP C 244 " --> pdb=" O MET C 175 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N THR C 177 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL C 242 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N PHE C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 60 through 63 removed outlier: 10.277A pdb=" N ASP D 29 " --> pdb=" O PRO D 73 " (cutoff:3.500A) removed outlier: 9.816A pdb=" N THR D 75 " --> pdb=" O ASP D 29 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL D 31 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N PHE D 77 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE D 33 " --> pdb=" O PHE D 77 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL D 8 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE D 33 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL D 95 " --> pdb=" O ILE D 120 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 208 through 210 removed outlier: 3.604A pdb=" N THR D 229 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG D 248 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY D 173 " --> pdb=" O THR D 246 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR D 246 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N MET D 175 " --> pdb=" O ASP D 244 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP D 244 " --> pdb=" O MET D 175 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N THR D 177 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL D 242 " --> pdb=" O THR D 177 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ILE D 311 " --> pdb=" O ASP D 296 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 208 through 210 removed outlier: 3.604A pdb=" N THR D 229 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG D 248 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY D 173 " --> pdb=" O THR D 246 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR D 246 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N MET D 175 " --> pdb=" O ASP D 244 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP D 244 " --> pdb=" O MET D 175 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N THR D 177 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL D 242 " --> pdb=" O THR D 177 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N PHE D 307 " --> pdb=" O LEU D 303 " (cutoff:3.500A) 520 hydrogen bonds defined for protein. 1368 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: 3.25 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3260 1.34 - 1.46: 1385 1.46 - 1.57: 5487 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 10216 Sorted by residual: bond pdb=" N VAL C 242 " pdb=" CA VAL C 242 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.11e-02 8.12e+03 1.28e+01 bond pdb=" N VAL B 242 " pdb=" CA VAL B 242 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.26e+01 bond pdb=" N VAL D 242 " pdb=" CA VAL D 242 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.26e+01 bond pdb=" N VAL A 242 " pdb=" CA VAL A 242 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.24e+01 bond pdb=" N VAL B 188 " pdb=" CA VAL B 188 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.15e-02 7.56e+03 1.14e+01 ... (remaining 10211 not shown) Histogram of bond angle deviations from ideal: 100.50 - 107.21: 319 107.21 - 113.92: 5845 113.92 - 120.63: 4015 120.63 - 127.34: 3569 127.34 - 134.05: 100 Bond angle restraints: 13848 Sorted by residual: angle pdb=" C ALA B 150 " pdb=" CA ALA B 150 " pdb=" CB ALA B 150 " ideal model delta sigma weight residual 116.63 110.81 5.82 1.16e+00 7.43e-01 2.52e+01 angle pdb=" C ALA D 150 " pdb=" CA ALA D 150 " pdb=" CB ALA D 150 " ideal model delta sigma weight residual 116.63 110.83 5.80 1.16e+00 7.43e-01 2.50e+01 angle pdb=" C ALA A 150 " pdb=" CA ALA A 150 " pdb=" CB ALA A 150 " ideal model delta sigma weight residual 116.63 110.83 5.80 1.16e+00 7.43e-01 2.50e+01 angle pdb=" C ALA C 150 " pdb=" CA ALA C 150 " pdb=" CB ALA C 150 " ideal model delta sigma weight residual 116.63 110.88 5.75 1.16e+00 7.43e-01 2.45e+01 angle pdb=" N ILE C 206 " pdb=" CA ILE C 206 " pdb=" C ILE C 206 " ideal model delta sigma weight residual 113.39 107.89 5.50 1.47e+00 4.63e-01 1.40e+01 ... (remaining 13843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 5408 16.89 - 33.78: 408 33.78 - 50.67: 160 50.67 - 67.56: 60 67.56 - 84.45: 8 Dihedral angle restraints: 6044 sinusoidal: 2268 harmonic: 3776 Sorted by residual: dihedral pdb=" CA ASP A 50 " pdb=" CB ASP A 50 " pdb=" CG ASP A 50 " pdb=" OD1 ASP A 50 " ideal model delta sinusoidal sigma weight residual -30.00 -84.76 54.76 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA ASP D 50 " pdb=" CB ASP D 50 " pdb=" CG ASP D 50 " pdb=" OD1 ASP D 50 " ideal model delta sinusoidal sigma weight residual -30.00 -84.72 54.72 1 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CA ASP B 50 " pdb=" CB ASP B 50 " pdb=" CG ASP B 50 " pdb=" OD1 ASP B 50 " ideal model delta sinusoidal sigma weight residual -30.00 -84.69 54.69 1 2.00e+01 2.50e-03 1.01e+01 ... (remaining 6041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1100 0.042 - 0.084: 310 0.084 - 0.127: 146 0.127 - 0.169: 14 0.169 - 0.211: 6 Chirality restraints: 1576 Sorted by residual: chirality pdb=" CA ILE C 206 " pdb=" N ILE C 206 " pdb=" C ILE C 206 " pdb=" CB ILE C 206 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE D 206 " pdb=" N ILE D 206 " pdb=" C ILE D 206 " pdb=" CB ILE D 206 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE A 206 " pdb=" N ILE A 206 " pdb=" C ILE A 206 " pdb=" CB ILE A 206 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1573 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 207 " -0.045 5.00e-02 4.00e+02 6.77e-02 7.33e+00 pdb=" N PRO D 208 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 208 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 208 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 207 " -0.045 5.00e-02 4.00e+02 6.76e-02 7.30e+00 pdb=" N PRO C 208 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 208 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 208 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 207 " 0.044 5.00e-02 4.00e+02 6.74e-02 7.27e+00 pdb=" N PRO B 208 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 208 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 208 " 0.036 5.00e-02 4.00e+02 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 301 2.72 - 3.26: 9851 3.26 - 3.81: 15900 3.81 - 4.35: 20720 4.35 - 4.90: 35089 Nonbonded interactions: 81861 Sorted by model distance: nonbonded pdb=" OH TYR C 94 " pdb=" OE2 GLU C 335 " model vdw 2.172 2.440 nonbonded pdb=" OH TYR B 94 " pdb=" OE2 GLU B 335 " model vdw 2.172 2.440 nonbonded pdb=" OH TYR D 94 " pdb=" OE2 GLU D 335 " model vdw 2.172 2.440 nonbonded pdb=" OH TYR A 94 " pdb=" OE2 GLU A 335 " model vdw 2.173 2.440 nonbonded pdb=" OE2 GLU C 172 " pdb=" NH1 ARG C 248 " model vdw 2.238 2.520 ... (remaining 81856 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' } 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: 0.590 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: 3.590 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.020 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 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 : 0.004 0.041 10216 Z= 0.272 Angle : 0.640 7.427 13848 Z= 0.418 Chirality : 0.049 0.211 1576 Planarity : 0.005 0.068 1796 Dihedral : 15.696 84.451 3636 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.76 % Allowed : 13.64 % Favored : 85.61 % 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 (0.25), residues: 1328 helix: 1.79 (0.26), residues: 392 sheet: -0.38 (0.36), residues: 232 loop : -0.03 (0.27), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 313 HIS 0.002 0.001 HIS A 53 PHE 0.007 0.001 PHE C 233 TYR 0.008 0.001 TYR B 314 ARG 0.006 0.001 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 170 time to evaluate : 1.096 Fit side-chains REVERT: A 29 ASP cc_start: 0.6871 (m-30) cc_final: 0.6466 (m-30) REVERT: A 37 PHE cc_start: 0.6293 (m-80) cc_final: 0.5841 (m-80) REVERT: A 57 HIS cc_start: 0.5836 (m-70) cc_final: 0.5613 (m170) REVERT: A 130 MET cc_start: 0.7661 (mtm) cc_final: 0.7311 (mtm) REVERT: A 138 GLU cc_start: 0.6885 (mm-30) cc_final: 0.5028 (pm20) REVERT: A 141 ASP cc_start: 0.5363 (p0) cc_final: 0.4807 (t0) REVERT: A 145 LYS cc_start: 0.6942 (mtmt) cc_final: 0.6634 (mmtt) REVERT: A 223 GLU cc_start: 0.5866 (mp0) cc_final: 0.5389 (mp0) REVERT: A 239 ASN cc_start: 0.5141 (OUTLIER) cc_final: 0.4854 (t0) REVERT: A 250 GLU cc_start: 0.6714 (tt0) cc_final: 0.5936 (tp30) REVERT: A 264 GLN cc_start: 0.6574 (tt0) cc_final: 0.5998 (mt0) REVERT: A 280 GLN cc_start: 0.6956 (mm-40) cc_final: 0.6736 (mm-40) REVERT: A 331 MET cc_start: 0.6669 (mtp) cc_final: 0.6316 (mtp) REVERT: B 29 ASP cc_start: 0.6852 (m-30) cc_final: 0.6456 (m-30) REVERT: B 37 PHE cc_start: 0.6285 (m-80) cc_final: 0.5813 (m-80) REVERT: B 57 HIS cc_start: 0.5823 (m-70) cc_final: 0.5607 (m170) REVERT: B 106 GLU cc_start: 0.6206 (tm-30) cc_final: 0.5393 (tp30) REVERT: B 130 MET cc_start: 0.7658 (mtm) cc_final: 0.7323 (mtm) REVERT: B 138 GLU cc_start: 0.6884 (mm-30) cc_final: 0.5014 (pm20) REVERT: B 141 ASP cc_start: 0.5326 (p0) cc_final: 0.4824 (t0) REVERT: B 145 LYS cc_start: 0.6905 (mtmt) cc_final: 0.6627 (mmtt) REVERT: B 223 GLU cc_start: 0.5876 (mp0) cc_final: 0.5383 (mp0) REVERT: B 239 ASN cc_start: 0.5162 (OUTLIER) cc_final: 0.4897 (t0) REVERT: B 250 GLU cc_start: 0.6646 (tt0) cc_final: 0.5889 (tp30) REVERT: B 264 GLN cc_start: 0.6524 (tt0) cc_final: 0.5959 (mt0) REVERT: B 280 GLN cc_start: 0.6962 (mm-40) cc_final: 0.6688 (mm-40) REVERT: B 331 MET cc_start: 0.6676 (mtp) cc_final: 0.6327 (mtp) REVERT: C 29 ASP cc_start: 0.6849 (m-30) cc_final: 0.6455 (m-30) REVERT: C 37 PHE cc_start: 0.6276 (m-80) cc_final: 0.5804 (m-80) REVERT: C 57 HIS cc_start: 0.5819 (m-70) cc_final: 0.5593 (m170) REVERT: C 106 GLU cc_start: 0.6243 (tm-30) cc_final: 0.5420 (tp30) REVERT: C 130 MET cc_start: 0.7657 (mtm) cc_final: 0.7322 (mtm) REVERT: C 138 GLU cc_start: 0.6883 (mm-30) cc_final: 0.5007 (pm20) REVERT: C 141 ASP cc_start: 0.5344 (p0) cc_final: 0.4828 (t0) REVERT: C 145 LYS cc_start: 0.6895 (mtmt) cc_final: 0.6619 (mmtt) REVERT: C 223 GLU cc_start: 0.5862 (mp0) cc_final: 0.5369 (mp0) REVERT: C 234 ARG cc_start: 0.6996 (mtt-85) cc_final: 0.6795 (mtt-85) REVERT: C 239 ASN cc_start: 0.5158 (OUTLIER) cc_final: 0.4883 (t0) REVERT: C 250 GLU cc_start: 0.6676 (tt0) cc_final: 0.5936 (tp30) REVERT: C 264 GLN cc_start: 0.6539 (tt0) cc_final: 0.5974 (mt0) REVERT: C 280 GLN cc_start: 0.6959 (mm-40) cc_final: 0.6685 (mm-40) REVERT: C 331 MET cc_start: 0.6664 (mtp) cc_final: 0.6313 (mtp) REVERT: D 29 ASP cc_start: 0.6869 (m-30) cc_final: 0.6454 (m-30) REVERT: D 37 PHE cc_start: 0.6305 (m-80) cc_final: 0.5828 (m-80) REVERT: D 57 HIS cc_start: 0.5835 (m-70) cc_final: 0.5612 (m170) REVERT: D 106 GLU cc_start: 0.6194 (tm-30) cc_final: 0.5380 (tp30) REVERT: D 130 MET cc_start: 0.7671 (mtm) cc_final: 0.7318 (mtm) REVERT: D 138 GLU cc_start: 0.6884 (mm-30) cc_final: 0.5019 (pm20) REVERT: D 141 ASP cc_start: 0.5302 (p0) cc_final: 0.4801 (t0) REVERT: D 145 LYS cc_start: 0.6869 (mtmt) cc_final: 0.6636 (mmtt) REVERT: D 223 GLU cc_start: 0.5885 (mp0) cc_final: 0.5400 (mp0) REVERT: D 239 ASN cc_start: 0.5162 (OUTLIER) cc_final: 0.4901 (t0) REVERT: D 250 GLU cc_start: 0.6667 (tt0) cc_final: 0.5909 (tp30) REVERT: D 264 GLN cc_start: 0.6546 (tt0) cc_final: 0.5981 (mt0) REVERT: D 280 GLN cc_start: 0.6962 (mm-40) cc_final: 0.6691 (mm-40) REVERT: D 331 MET cc_start: 0.6685 (mtp) cc_final: 0.6321 (mtp) outliers start: 8 outliers final: 0 residues processed: 174 average time/residue: 1.4278 time to fit residues: 263.2086 Evaluate side-chains 132 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain C residue 239 ASN Chi-restraints excluded: chain D residue 239 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 62 optimal weight: 0.0980 chunk 77 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 239 ASN B 142 ASN B 239 ASN C 142 ASN C 239 ASN D 142 ASN D 239 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 10216 Z= 0.170 Angle : 0.590 7.498 13848 Z= 0.327 Chirality : 0.048 0.198 1576 Planarity : 0.005 0.059 1796 Dihedral : 4.692 25.076 1420 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.70 % Allowed : 11.55 % Favored : 86.74 % 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 (0.25), residues: 1328 helix: 1.61 (0.26), residues: 396 sheet: -0.02 (0.37), residues: 216 loop : -0.16 (0.26), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 87 HIS 0.004 0.001 HIS A 53 PHE 0.011 0.001 PHE D 233 TYR 0.016 0.002 TYR B 42 ARG 0.005 0.000 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 1.158 Fit side-chains REVERT: A 29 ASP cc_start: 0.6854 (m-30) cc_final: 0.6479 (m-30) REVERT: A 37 PHE cc_start: 0.6625 (m-80) cc_final: 0.6112 (m-80) REVERT: A 57 HIS cc_start: 0.5737 (m-70) cc_final: 0.5527 (m170) REVERT: A 107 LYS cc_start: 0.6312 (mttt) cc_final: 0.6021 (mtpp) REVERT: A 130 MET cc_start: 0.7664 (mtm) cc_final: 0.7271 (mtm) REVERT: A 138 GLU cc_start: 0.6855 (mm-30) cc_final: 0.5089 (pm20) REVERT: A 143 SER cc_start: 0.6835 (m) cc_final: 0.6075 (p) REVERT: A 145 LYS cc_start: 0.7285 (mtmt) cc_final: 0.6946 (mmtt) REVERT: A 223 GLU cc_start: 0.5823 (mp0) cc_final: 0.5393 (mp0) REVERT: A 250 GLU cc_start: 0.6698 (tt0) cc_final: 0.5977 (mt-10) REVERT: A 264 GLN cc_start: 0.6435 (tt0) cc_final: 0.5887 (mt0) REVERT: A 280 GLN cc_start: 0.6997 (mm-40) cc_final: 0.6755 (mm-40) REVERT: A 331 MET cc_start: 0.6777 (mtp) cc_final: 0.6474 (mtp) REVERT: B 29 ASP cc_start: 0.6884 (m-30) cc_final: 0.6498 (m-30) REVERT: B 37 PHE cc_start: 0.6575 (m-80) cc_final: 0.6058 (m-80) REVERT: B 57 HIS cc_start: 0.5740 (m-70) cc_final: 0.5534 (m170) REVERT: B 107 LYS cc_start: 0.6327 (mttt) cc_final: 0.6066 (mtpp) REVERT: B 130 MET cc_start: 0.7664 (mtm) cc_final: 0.7273 (mtm) REVERT: B 138 GLU cc_start: 0.6851 (mm-30) cc_final: 0.5084 (pm20) REVERT: B 143 SER cc_start: 0.6850 (m) cc_final: 0.6083 (p) REVERT: B 145 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6972 (mmtt) REVERT: B 223 GLU cc_start: 0.5804 (mp0) cc_final: 0.5384 (mp0) REVERT: B 250 GLU cc_start: 0.6698 (tt0) cc_final: 0.6045 (mm-30) REVERT: B 264 GLN cc_start: 0.6432 (tt0) cc_final: 0.5885 (mt0) REVERT: B 280 GLN cc_start: 0.7002 (mm-40) cc_final: 0.6760 (mm-40) REVERT: B 331 MET cc_start: 0.6790 (mtp) cc_final: 0.6486 (mtp) REVERT: C 29 ASP cc_start: 0.6883 (m-30) cc_final: 0.6495 (m-30) REVERT: C 37 PHE cc_start: 0.6573 (m-80) cc_final: 0.6056 (m-80) REVERT: C 57 HIS cc_start: 0.5738 (m-70) cc_final: 0.5534 (m170) REVERT: C 107 LYS cc_start: 0.6328 (mttt) cc_final: 0.6065 (mtpp) REVERT: C 130 MET cc_start: 0.7667 (mtm) cc_final: 0.7276 (mtm) REVERT: C 138 GLU cc_start: 0.6853 (mm-30) cc_final: 0.5087 (pm20) REVERT: C 143 SER cc_start: 0.6851 (m) cc_final: 0.6082 (p) REVERT: C 145 LYS cc_start: 0.7326 (mtmt) cc_final: 0.6999 (mmtt) REVERT: C 250 GLU cc_start: 0.6698 (tt0) cc_final: 0.6045 (mm-30) REVERT: C 264 GLN cc_start: 0.6432 (tt0) cc_final: 0.5884 (mt0) REVERT: C 280 GLN cc_start: 0.7002 (mm-40) cc_final: 0.6761 (mm-40) REVERT: C 331 MET cc_start: 0.6793 (mtp) cc_final: 0.6487 (mtp) REVERT: D 29 ASP cc_start: 0.6858 (m-30) cc_final: 0.6483 (m-30) REVERT: D 37 PHE cc_start: 0.6575 (m-80) cc_final: 0.6057 (m-80) REVERT: D 57 HIS cc_start: 0.5740 (m-70) cc_final: 0.5531 (m170) REVERT: D 107 LYS cc_start: 0.6359 (mttt) cc_final: 0.6104 (mtpp) REVERT: D 130 MET cc_start: 0.7664 (mtm) cc_final: 0.7385 (mtm) REVERT: D 138 GLU cc_start: 0.6844 (mm-30) cc_final: 0.5088 (pm20) REVERT: D 143 SER cc_start: 0.6811 (m) cc_final: 0.6058 (p) REVERT: D 145 LYS cc_start: 0.7312 (mtmt) cc_final: 0.6995 (mmtt) REVERT: D 223 GLU cc_start: 0.5747 (mp0) cc_final: 0.5335 (mp0) REVERT: D 250 GLU cc_start: 0.6700 (tt0) cc_final: 0.6047 (mm-30) REVERT: D 264 GLN cc_start: 0.6432 (tt0) cc_final: 0.5887 (mt0) REVERT: D 280 GLN cc_start: 0.7001 (mm-40) cc_final: 0.6762 (mm-40) REVERT: D 331 MET cc_start: 0.6782 (mtp) cc_final: 0.6477 (mtp) outliers start: 18 outliers final: 8 residues processed: 151 average time/residue: 1.2715 time to fit residues: 205.2824 Evaluate side-chains 135 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 333 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 81 optimal weight: 0.8980 chunk 33 optimal weight: 20.0000 chunk 120 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10216 Z= 0.332 Angle : 0.810 9.125 13848 Z= 0.454 Chirality : 0.057 0.346 1576 Planarity : 0.008 0.070 1796 Dihedral : 5.150 17.616 1412 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.71 % Favored : 96.99 % Rotamer: Outliers : 1.89 % Allowed : 11.93 % Favored : 86.17 % 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: 0.39 (0.24), residues: 1328 helix: 1.14 (0.25), residues: 392 sheet: -0.56 (0.36), residues: 196 loop : 0.12 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 313 HIS 0.006 0.002 HIS C 57 PHE 0.017 0.003 PHE C 233 TYR 0.019 0.003 TYR B 314 ARG 0.004 0.001 ARG D 323 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.209 Fit side-chains REVERT: A 29 ASP cc_start: 0.6791 (m-30) cc_final: 0.6495 (m-30) REVERT: A 107 LYS cc_start: 0.6207 (mttt) cc_final: 0.5959 (mtpp) REVERT: A 130 MET cc_start: 0.7649 (mtm) cc_final: 0.7407 (mtm) REVERT: A 138 GLU cc_start: 0.6892 (mm-30) cc_final: 0.5290 (pm20) REVERT: A 143 SER cc_start: 0.6660 (m) cc_final: 0.6328 (p) REVERT: A 145 LYS cc_start: 0.7450 (mtmt) cc_final: 0.7059 (mmtm) REVERT: A 250 GLU cc_start: 0.6731 (tt0) cc_final: 0.6063 (mt-10) REVERT: A 264 GLN cc_start: 0.6538 (tt0) cc_final: 0.6008 (mt0) REVERT: A 280 GLN cc_start: 0.7112 (mm-40) cc_final: 0.6846 (mm-40) REVERT: A 331 MET cc_start: 0.6713 (mtp) cc_final: 0.6376 (mtp) REVERT: B 29 ASP cc_start: 0.6791 (m-30) cc_final: 0.6498 (m-30) REVERT: B 130 MET cc_start: 0.7649 (mtm) cc_final: 0.7407 (mtm) REVERT: B 138 GLU cc_start: 0.6893 (mm-30) cc_final: 0.5292 (pm20) REVERT: B 143 SER cc_start: 0.6654 (m) cc_final: 0.6321 (p) REVERT: B 145 LYS cc_start: 0.7436 (mtmt) cc_final: 0.7057 (mmtm) REVERT: B 250 GLU cc_start: 0.6727 (tt0) cc_final: 0.6151 (mm-30) REVERT: B 264 GLN cc_start: 0.6534 (tt0) cc_final: 0.6004 (mt0) REVERT: B 280 GLN cc_start: 0.7112 (mm-40) cc_final: 0.6845 (mm-40) REVERT: B 331 MET cc_start: 0.6706 (mtp) cc_final: 0.6361 (mtp) REVERT: C 29 ASP cc_start: 0.6792 (m-30) cc_final: 0.6497 (m-30) REVERT: C 130 MET cc_start: 0.7644 (mtm) cc_final: 0.7402 (mtm) REVERT: C 138 GLU cc_start: 0.6893 (mm-30) cc_final: 0.5293 (pm20) REVERT: C 143 SER cc_start: 0.6662 (m) cc_final: 0.6327 (p) REVERT: C 145 LYS cc_start: 0.7438 (mtmt) cc_final: 0.7055 (mmtm) REVERT: C 250 GLU cc_start: 0.6727 (tt0) cc_final: 0.6152 (mm-30) REVERT: C 264 GLN cc_start: 0.6528 (tt0) cc_final: 0.5999 (mt0) REVERT: C 280 GLN cc_start: 0.7112 (mm-40) cc_final: 0.6846 (mm-40) REVERT: C 331 MET cc_start: 0.6704 (mtp) cc_final: 0.6358 (mtp) REVERT: D 29 ASP cc_start: 0.6791 (m-30) cc_final: 0.6496 (m-30) REVERT: D 64 ASN cc_start: 0.6600 (m110) cc_final: 0.5787 (t0) REVERT: D 130 MET cc_start: 0.7643 (mtm) cc_final: 0.7401 (mtm) REVERT: D 138 GLU cc_start: 0.6891 (mm-30) cc_final: 0.5292 (pm20) REVERT: D 143 SER cc_start: 0.6666 (m) cc_final: 0.6331 (p) REVERT: D 145 LYS cc_start: 0.7436 (mtmt) cc_final: 0.7054 (mmtm) REVERT: D 250 GLU cc_start: 0.6725 (tt0) cc_final: 0.6149 (mm-30) REVERT: D 264 GLN cc_start: 0.6536 (tt0) cc_final: 0.6004 (mt0) REVERT: D 280 GLN cc_start: 0.7110 (mm-40) cc_final: 0.6845 (mm-40) REVERT: D 331 MET cc_start: 0.6691 (mtp) cc_final: 0.6354 (mtp) outliers start: 20 outliers final: 20 residues processed: 124 average time/residue: 1.5383 time to fit residues: 202.4844 Evaluate side-chains 129 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 333 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10216 Z= 0.217 Angle : 0.659 8.137 13848 Z= 0.369 Chirality : 0.050 0.264 1576 Planarity : 0.006 0.060 1796 Dihedral : 4.954 18.101 1412 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.89 % Allowed : 12.50 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.24), residues: 1328 helix: 1.31 (0.26), residues: 392 sheet: -0.31 (0.40), residues: 176 loop : 0.02 (0.25), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 87 HIS 0.004 0.001 HIS D 53 PHE 0.015 0.002 PHE A 233 TYR 0.016 0.002 TYR B 314 ARG 0.002 0.000 ARG C 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 1.128 Fit side-chains REVERT: A 29 ASP cc_start: 0.6893 (m-30) cc_final: 0.6587 (m-30) REVERT: A 107 LYS cc_start: 0.6124 (mttt) cc_final: 0.5920 (mtpp) REVERT: A 130 MET cc_start: 0.7663 (mtm) cc_final: 0.7413 (mtm) REVERT: A 138 GLU cc_start: 0.6918 (mm-30) cc_final: 0.5284 (pm20) REVERT: A 143 SER cc_start: 0.6666 (m) cc_final: 0.6350 (p) REVERT: A 145 LYS cc_start: 0.7439 (mtmt) cc_final: 0.7011 (mmtt) REVERT: A 250 GLU cc_start: 0.6795 (tt0) cc_final: 0.6115 (mt-10) REVERT: A 264 GLN cc_start: 0.6577 (tt0) cc_final: 0.6056 (mt0) REVERT: A 280 GLN cc_start: 0.7083 (mm-40) cc_final: 0.6797 (mm-40) REVERT: A 331 MET cc_start: 0.6733 (mtp) cc_final: 0.6294 (mtp) REVERT: B 29 ASP cc_start: 0.6894 (m-30) cc_final: 0.6590 (m-30) REVERT: B 130 MET cc_start: 0.7670 (mtm) cc_final: 0.7420 (mtm) REVERT: B 138 GLU cc_start: 0.6919 (mm-30) cc_final: 0.5286 (pm20) REVERT: B 143 SER cc_start: 0.6667 (m) cc_final: 0.6357 (p) REVERT: B 145 LYS cc_start: 0.7449 (mtmt) cc_final: 0.7031 (mmtt) REVERT: B 250 GLU cc_start: 0.6795 (tt0) cc_final: 0.6246 (mm-30) REVERT: B 264 GLN cc_start: 0.6574 (tt0) cc_final: 0.6053 (mt0) REVERT: B 280 GLN cc_start: 0.7083 (mm-40) cc_final: 0.6797 (mm-40) REVERT: B 331 MET cc_start: 0.6734 (mtp) cc_final: 0.6296 (mtp) REVERT: C 29 ASP cc_start: 0.6894 (m-30) cc_final: 0.6588 (m-30) REVERT: C 130 MET cc_start: 0.7672 (mtm) cc_final: 0.7422 (mtm) REVERT: C 138 GLU cc_start: 0.6918 (mm-30) cc_final: 0.5286 (pm20) REVERT: C 143 SER cc_start: 0.6668 (m) cc_final: 0.6350 (p) REVERT: C 145 LYS cc_start: 0.7449 (mtmt) cc_final: 0.7026 (mmtt) REVERT: C 250 GLU cc_start: 0.6796 (tt0) cc_final: 0.6247 (mm-30) REVERT: C 264 GLN cc_start: 0.6575 (tt0) cc_final: 0.6054 (mt0) REVERT: C 280 GLN cc_start: 0.7082 (mm-40) cc_final: 0.6797 (mm-40) REVERT: C 331 MET cc_start: 0.6732 (mtp) cc_final: 0.6294 (mtp) REVERT: D 29 ASP cc_start: 0.6893 (m-30) cc_final: 0.6588 (m-30) REVERT: D 130 MET cc_start: 0.7662 (mtm) cc_final: 0.7412 (mtm) REVERT: D 138 GLU cc_start: 0.6916 (mm-30) cc_final: 0.5286 (pm20) REVERT: D 143 SER cc_start: 0.6670 (m) cc_final: 0.6351 (p) REVERT: D 145 LYS cc_start: 0.7446 (mtmt) cc_final: 0.7025 (mmtt) REVERT: D 250 GLU cc_start: 0.6794 (tt0) cc_final: 0.6245 (mm-30) REVERT: D 264 GLN cc_start: 0.6576 (tt0) cc_final: 0.6052 (mt0) REVERT: D 280 GLN cc_start: 0.7081 (mm-40) cc_final: 0.6797 (mm-40) REVERT: D 331 MET cc_start: 0.6734 (mtp) cc_final: 0.6295 (mtp) outliers start: 20 outliers final: 16 residues processed: 132 average time/residue: 1.3526 time to fit residues: 190.6536 Evaluate side-chains 128 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 333 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10216 Z= 0.241 Angle : 0.700 8.919 13848 Z= 0.392 Chirality : 0.052 0.297 1576 Planarity : 0.006 0.064 1796 Dihedral : 5.077 18.342 1412 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.65 % Allowed : 12.12 % Favored : 85.23 % 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: 0.39 (0.24), residues: 1328 helix: 1.26 (0.26), residues: 392 sheet: -0.34 (0.39), residues: 176 loop : -0.04 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 313 HIS 0.005 0.001 HIS A 53 PHE 0.016 0.002 PHE A 233 TYR 0.016 0.002 TYR A 314 ARG 0.003 0.001 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 1.044 Fit side-chains REVERT: A 29 ASP cc_start: 0.6907 (m-30) cc_final: 0.6610 (m-30) REVERT: A 113 GLN cc_start: 0.5929 (OUTLIER) cc_final: 0.5708 (mt0) REVERT: A 130 MET cc_start: 0.7667 (mtm) cc_final: 0.7417 (mtm) REVERT: A 138 GLU cc_start: 0.6879 (mm-30) cc_final: 0.5296 (pm20) REVERT: A 143 SER cc_start: 0.6679 (m) cc_final: 0.6370 (p) REVERT: A 145 LYS cc_start: 0.7464 (mtmt) cc_final: 0.7001 (mmtt) REVERT: A 194 LYS cc_start: 0.5243 (OUTLIER) cc_final: 0.4918 (mmmm) REVERT: A 250 GLU cc_start: 0.6841 (tt0) cc_final: 0.6098 (mt-10) REVERT: A 260 LYS cc_start: 0.6606 (ttmm) cc_final: 0.5783 (ttpp) REVERT: A 264 GLN cc_start: 0.6479 (tt0) cc_final: 0.5952 (mt0) REVERT: A 280 GLN cc_start: 0.7092 (mm-40) cc_final: 0.6824 (mm-40) REVERT: A 331 MET cc_start: 0.6721 (mtp) cc_final: 0.6322 (mtp) REVERT: B 29 ASP cc_start: 0.6907 (m-30) cc_final: 0.6613 (m-30) REVERT: B 113 GLN cc_start: 0.5929 (OUTLIER) cc_final: 0.5707 (mt0) REVERT: B 130 MET cc_start: 0.7667 (mtm) cc_final: 0.7417 (mtm) REVERT: B 138 GLU cc_start: 0.6879 (mm-30) cc_final: 0.5297 (pm20) REVERT: B 143 SER cc_start: 0.6679 (m) cc_final: 0.6373 (p) REVERT: B 145 LYS cc_start: 0.7465 (mtmt) cc_final: 0.7009 (mmtt) REVERT: B 194 LYS cc_start: 0.5320 (OUTLIER) cc_final: 0.4988 (mmmm) REVERT: B 250 GLU cc_start: 0.6848 (tt0) cc_final: 0.6298 (mm-30) REVERT: B 260 LYS cc_start: 0.6606 (ttmm) cc_final: 0.5782 (ttpp) REVERT: B 264 GLN cc_start: 0.6478 (tt0) cc_final: 0.5951 (mt0) REVERT: B 280 GLN cc_start: 0.7140 (mm-40) cc_final: 0.6856 (mm-40) REVERT: B 331 MET cc_start: 0.6713 (mtp) cc_final: 0.6314 (mtp) REVERT: C 29 ASP cc_start: 0.6908 (m-30) cc_final: 0.6608 (m-30) REVERT: C 113 GLN cc_start: 0.5932 (OUTLIER) cc_final: 0.5709 (mt0) REVERT: C 130 MET cc_start: 0.7670 (mtm) cc_final: 0.7419 (mtm) REVERT: C 138 GLU cc_start: 0.6878 (mm-30) cc_final: 0.5298 (pm20) REVERT: C 143 SER cc_start: 0.6680 (m) cc_final: 0.6369 (p) REVERT: C 145 LYS cc_start: 0.7465 (mtmt) cc_final: 0.7007 (mmtt) REVERT: C 194 LYS cc_start: 0.5321 (OUTLIER) cc_final: 0.4985 (mmmm) REVERT: C 250 GLU cc_start: 0.6851 (tt0) cc_final: 0.6299 (mm-30) REVERT: C 260 LYS cc_start: 0.6604 (ttmm) cc_final: 0.5781 (ttpp) REVERT: C 264 GLN cc_start: 0.6478 (tt0) cc_final: 0.5950 (mt0) REVERT: C 280 GLN cc_start: 0.7131 (mm-40) cc_final: 0.6847 (mm-40) REVERT: C 331 MET cc_start: 0.6712 (mtp) cc_final: 0.6313 (mtp) REVERT: D 29 ASP cc_start: 0.6907 (m-30) cc_final: 0.6611 (m-30) REVERT: D 113 GLN cc_start: 0.5928 (OUTLIER) cc_final: 0.5706 (mt0) REVERT: D 130 MET cc_start: 0.7667 (mtm) cc_final: 0.7400 (mtm) REVERT: D 138 GLU cc_start: 0.6877 (mm-30) cc_final: 0.5298 (pm20) REVERT: D 143 SER cc_start: 0.6682 (m) cc_final: 0.6370 (p) REVERT: D 145 LYS cc_start: 0.7462 (mtmt) cc_final: 0.7004 (mmtt) REVERT: D 194 LYS cc_start: 0.5319 (OUTLIER) cc_final: 0.4987 (mmmm) REVERT: D 250 GLU cc_start: 0.6840 (tt0) cc_final: 0.6297 (mm-30) REVERT: D 260 LYS cc_start: 0.6606 (ttmm) cc_final: 0.5783 (ttpp) REVERT: D 264 GLN cc_start: 0.6479 (tt0) cc_final: 0.5951 (mt0) REVERT: D 280 GLN cc_start: 0.7138 (mm-40) cc_final: 0.6855 (mm-40) REVERT: D 331 MET cc_start: 0.6722 (mtp) cc_final: 0.6323 (mtp) outliers start: 28 outliers final: 20 residues processed: 142 average time/residue: 1.4603 time to fit residues: 220.1290 Evaluate side-chains 145 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 194 LYS Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 333 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10216 Z= 0.300 Angle : 0.781 10.199 13848 Z= 0.437 Chirality : 0.055 0.318 1576 Planarity : 0.007 0.068 1796 Dihedral : 5.246 18.738 1412 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.41 % Allowed : 12.59 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.23), residues: 1328 helix: 1.06 (0.25), residues: 392 sheet: -0.47 (0.39), residues: 176 loop : -0.11 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 313 HIS 0.006 0.001 HIS D 53 PHE 0.018 0.003 PHE A 233 TYR 0.017 0.003 TYR B 314 ARG 0.003 0.001 ARG C 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 120 time to evaluate : 1.099 Fit side-chains REVERT: A 29 ASP cc_start: 0.6912 (m-30) cc_final: 0.6632 (m-30) REVERT: A 64 ASN cc_start: 0.6543 (m110) cc_final: 0.5774 (t0) REVERT: A 113 GLN cc_start: 0.5870 (OUTLIER) cc_final: 0.5648 (mt0) REVERT: A 130 MET cc_start: 0.7658 (mtm) cc_final: 0.7404 (mtm) REVERT: A 138 GLU cc_start: 0.6878 (mm-30) cc_final: 0.5259 (pm20) REVERT: A 143 SER cc_start: 0.6710 (m) cc_final: 0.6379 (p) REVERT: A 194 LYS cc_start: 0.5356 (OUTLIER) cc_final: 0.5041 (mmmm) REVERT: A 250 GLU cc_start: 0.6844 (tt0) cc_final: 0.6098 (mt-10) REVERT: A 260 LYS cc_start: 0.6625 (ttmm) cc_final: 0.5799 (ttpp) REVERT: A 264 GLN cc_start: 0.6505 (tt0) cc_final: 0.5972 (mt0) REVERT: A 280 GLN cc_start: 0.7155 (mm-40) cc_final: 0.6894 (mm-40) REVERT: B 29 ASP cc_start: 0.6911 (m-30) cc_final: 0.6634 (m-30) REVERT: B 64 ASN cc_start: 0.6539 (m110) cc_final: 0.5772 (t0) REVERT: B 113 GLN cc_start: 0.5870 (OUTLIER) cc_final: 0.5646 (mt0) REVERT: B 130 MET cc_start: 0.7658 (mtm) cc_final: 0.7403 (mtm) REVERT: B 138 GLU cc_start: 0.6879 (mm-30) cc_final: 0.5260 (pm20) REVERT: B 143 SER cc_start: 0.6699 (m) cc_final: 0.6362 (p) REVERT: B 145 LYS cc_start: 0.7523 (mtmt) cc_final: 0.7067 (mmtm) REVERT: B 194 LYS cc_start: 0.5439 (OUTLIER) cc_final: 0.5118 (mmmm) REVERT: B 250 GLU cc_start: 0.6826 (tt0) cc_final: 0.6290 (mm-30) REVERT: B 260 LYS cc_start: 0.6626 (ttmm) cc_final: 0.5799 (ttpp) REVERT: B 264 GLN cc_start: 0.6510 (tt0) cc_final: 0.5978 (mt0) REVERT: B 280 GLN cc_start: 0.7168 (mm-40) cc_final: 0.6897 (mm-40) REVERT: C 29 ASP cc_start: 0.6913 (m-30) cc_final: 0.6632 (m-30) REVERT: C 64 ASN cc_start: 0.6540 (m110) cc_final: 0.5772 (t0) REVERT: C 113 GLN cc_start: 0.5872 (OUTLIER) cc_final: 0.5647 (mt0) REVERT: C 130 MET cc_start: 0.7661 (mtm) cc_final: 0.7406 (mtm) REVERT: C 138 GLU cc_start: 0.6878 (mm-30) cc_final: 0.5261 (pm20) REVERT: C 143 SER cc_start: 0.6711 (m) cc_final: 0.6379 (p) REVERT: C 194 LYS cc_start: 0.5368 (OUTLIER) cc_final: 0.5054 (mmmm) REVERT: C 250 GLU cc_start: 0.6827 (tt0) cc_final: 0.6291 (mm-30) REVERT: C 260 LYS cc_start: 0.6623 (ttmm) cc_final: 0.5797 (ttpp) REVERT: C 264 GLN cc_start: 0.6510 (tt0) cc_final: 0.5979 (mt0) REVERT: C 280 GLN cc_start: 0.7168 (mm-40) cc_final: 0.6898 (mm-40) REVERT: D 29 ASP cc_start: 0.6912 (m-30) cc_final: 0.6633 (m-30) REVERT: D 64 ASN cc_start: 0.6544 (m110) cc_final: 0.5774 (t0) REVERT: D 113 GLN cc_start: 0.5869 (OUTLIER) cc_final: 0.5646 (mt0) REVERT: D 138 GLU cc_start: 0.6877 (mm-30) cc_final: 0.5262 (pm20) REVERT: D 143 SER cc_start: 0.6713 (m) cc_final: 0.6380 (p) REVERT: D 194 LYS cc_start: 0.5439 (OUTLIER) cc_final: 0.5118 (mmmm) REVERT: D 250 GLU cc_start: 0.6824 (tt0) cc_final: 0.6289 (mm-30) REVERT: D 260 LYS cc_start: 0.6624 (ttmm) cc_final: 0.5798 (ttpp) REVERT: D 264 GLN cc_start: 0.6512 (tt0) cc_final: 0.5977 (mt0) REVERT: D 280 GLN cc_start: 0.7167 (mm-40) cc_final: 0.6897 (mm-40) outliers start: 36 outliers final: 20 residues processed: 152 average time/residue: 1.4460 time to fit residues: 233.7311 Evaluate side-chains 145 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 194 LYS Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 333 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10216 Z= 0.271 Angle : 0.738 9.357 13848 Z= 0.414 Chirality : 0.052 0.215 1576 Planarity : 0.007 0.065 1796 Dihedral : 5.264 18.762 1412 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.65 % Allowed : 13.64 % Favored : 83.71 % 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: 0.21 (0.23), residues: 1328 helix: 1.10 (0.25), residues: 392 sheet: -0.43 (0.39), residues: 176 loop : -0.15 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 313 HIS 0.005 0.001 HIS C 53 PHE 0.018 0.002 PHE B 233 TYR 0.016 0.002 TYR A 314 ARG 0.003 0.001 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 1.165 Fit side-chains REVERT: A 29 ASP cc_start: 0.6910 (m-30) cc_final: 0.6640 (m-30) REVERT: A 113 GLN cc_start: 0.5929 (OUTLIER) cc_final: 0.5703 (mt0) REVERT: A 138 GLU cc_start: 0.6878 (mm-30) cc_final: 0.5265 (pm20) REVERT: A 143 SER cc_start: 0.6722 (m) cc_final: 0.6387 (p) REVERT: A 194 LYS cc_start: 0.5316 (OUTLIER) cc_final: 0.4996 (mmmm) REVERT: A 250 GLU cc_start: 0.6832 (tt0) cc_final: 0.6090 (mt-10) REVERT: A 260 LYS cc_start: 0.6622 (ttmm) cc_final: 0.5798 (ttpp) REVERT: A 264 GLN cc_start: 0.6512 (tt0) cc_final: 0.5976 (mt0) REVERT: A 280 GLN cc_start: 0.7169 (mm-40) cc_final: 0.6901 (mm-40) REVERT: B 29 ASP cc_start: 0.6910 (m-30) cc_final: 0.6641 (m-30) REVERT: B 113 GLN cc_start: 0.5929 (OUTLIER) cc_final: 0.5701 (mt0) REVERT: B 138 GLU cc_start: 0.6881 (mm-30) cc_final: 0.5299 (pm20) REVERT: B 143 SER cc_start: 0.6709 (m) cc_final: 0.6375 (p) REVERT: B 145 LYS cc_start: 0.7517 (mtmt) cc_final: 0.7032 (mmtt) REVERT: B 194 LYS cc_start: 0.5344 (OUTLIER) cc_final: 0.5032 (mmmm) REVERT: B 250 GLU cc_start: 0.6831 (tt0) cc_final: 0.6282 (mm-30) REVERT: B 260 LYS cc_start: 0.6623 (ttmm) cc_final: 0.5798 (ttpp) REVERT: B 264 GLN cc_start: 0.6510 (tt0) cc_final: 0.5975 (mt0) REVERT: B 280 GLN cc_start: 0.7197 (mm-40) cc_final: 0.6932 (mm-40) REVERT: C 29 ASP cc_start: 0.6911 (m-30) cc_final: 0.6639 (m-30) REVERT: C 113 GLN cc_start: 0.5960 (OUTLIER) cc_final: 0.5732 (mt0) REVERT: C 138 GLU cc_start: 0.6880 (mm-30) cc_final: 0.5300 (pm20) REVERT: C 143 SER cc_start: 0.6734 (m) cc_final: 0.6400 (p) REVERT: C 194 LYS cc_start: 0.5329 (OUTLIER) cc_final: 0.5010 (mmmm) REVERT: C 250 GLU cc_start: 0.6833 (tt0) cc_final: 0.6284 (mm-30) REVERT: C 260 LYS cc_start: 0.6621 (ttmm) cc_final: 0.5797 (ttpp) REVERT: C 264 GLN cc_start: 0.6510 (tt0) cc_final: 0.5975 (mt0) REVERT: C 280 GLN cc_start: 0.7198 (mm-40) cc_final: 0.6934 (mm-40) REVERT: D 29 ASP cc_start: 0.6910 (m-30) cc_final: 0.6641 (m-30) REVERT: D 113 GLN cc_start: 0.5959 (OUTLIER) cc_final: 0.5732 (mt0) REVERT: D 138 GLU cc_start: 0.6877 (mm-30) cc_final: 0.5299 (pm20) REVERT: D 143 SER cc_start: 0.6724 (m) cc_final: 0.6387 (p) REVERT: D 194 LYS cc_start: 0.5343 (OUTLIER) cc_final: 0.5032 (mmmm) REVERT: D 250 GLU cc_start: 0.6831 (tt0) cc_final: 0.6282 (mm-30) REVERT: D 260 LYS cc_start: 0.6622 (ttmm) cc_final: 0.5798 (ttpp) REVERT: D 264 GLN cc_start: 0.6512 (tt0) cc_final: 0.5974 (mt0) REVERT: D 280 GLN cc_start: 0.7196 (mm-40) cc_final: 0.6931 (mm-40) outliers start: 28 outliers final: 20 residues processed: 141 average time/residue: 1.4638 time to fit residues: 219.1614 Evaluate side-chains 141 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 194 LYS Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 333 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 10216 Z= 0.189 Angle : 0.628 7.901 13848 Z= 0.350 Chirality : 0.048 0.175 1576 Planarity : 0.006 0.068 1796 Dihedral : 5.035 18.716 1412 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.65 % Allowed : 13.64 % Favored : 83.71 % 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: 0.46 (0.24), residues: 1328 helix: 1.41 (0.26), residues: 392 sheet: -0.23 (0.40), residues: 176 loop : -0.08 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 87 HIS 0.003 0.001 HIS D 53 PHE 0.015 0.002 PHE C 233 TYR 0.014 0.002 TYR B 314 ARG 0.002 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 1.066 Fit side-chains REVERT: A 29 ASP cc_start: 0.6918 (m-30) cc_final: 0.6626 (m-30) REVERT: A 138 GLU cc_start: 0.6842 (mm-30) cc_final: 0.5229 (pm20) REVERT: A 143 SER cc_start: 0.6697 (m) cc_final: 0.6401 (p) REVERT: A 194 LYS cc_start: 0.5325 (OUTLIER) cc_final: 0.4873 (mmtm) REVERT: A 250 GLU cc_start: 0.6839 (tt0) cc_final: 0.6088 (mt-10) REVERT: A 260 LYS cc_start: 0.6630 (ttmm) cc_final: 0.5813 (ttpp) REVERT: A 264 GLN cc_start: 0.6564 (tt0) cc_final: 0.6046 (mt0) REVERT: A 280 GLN cc_start: 0.7111 (mm-40) cc_final: 0.6834 (mm-40) REVERT: B 29 ASP cc_start: 0.6919 (m-30) cc_final: 0.6627 (m-30) REVERT: B 138 GLU cc_start: 0.6843 (mm-30) cc_final: 0.5230 (pm20) REVERT: B 143 SER cc_start: 0.6692 (m) cc_final: 0.6399 (p) REVERT: B 145 LYS cc_start: 0.7472 (mtmt) cc_final: 0.7000 (mmtt) REVERT: B 194 LYS cc_start: 0.5272 (OUTLIER) cc_final: 0.4812 (mmtm) REVERT: B 250 GLU cc_start: 0.6839 (tt0) cc_final: 0.6295 (mm-30) REVERT: B 260 LYS cc_start: 0.6629 (ttmm) cc_final: 0.5812 (ttpp) REVERT: B 264 GLN cc_start: 0.6564 (tt0) cc_final: 0.6045 (mt0) REVERT: B 280 GLN cc_start: 0.7111 (mm-40) cc_final: 0.6833 (mm-40) REVERT: C 29 ASP cc_start: 0.6895 (m-30) cc_final: 0.6626 (m-30) REVERT: C 113 GLN cc_start: 0.5954 (OUTLIER) cc_final: 0.5729 (mt0) REVERT: C 138 GLU cc_start: 0.6842 (mm-30) cc_final: 0.5230 (pm20) REVERT: C 143 SER cc_start: 0.6698 (m) cc_final: 0.6401 (p) REVERT: C 194 LYS cc_start: 0.5220 (OUTLIER) cc_final: 0.4767 (mmtm) REVERT: C 250 GLU cc_start: 0.6840 (tt0) cc_final: 0.6297 (mm-30) REVERT: C 260 LYS cc_start: 0.6628 (ttmm) cc_final: 0.5812 (ttpp) REVERT: C 264 GLN cc_start: 0.6564 (tt0) cc_final: 0.6046 (mt0) REVERT: C 280 GLN cc_start: 0.7111 (mm-40) cc_final: 0.6834 (mm-40) REVERT: D 29 ASP cc_start: 0.6918 (m-30) cc_final: 0.6627 (m-30) REVERT: D 138 GLU cc_start: 0.6840 (mm-30) cc_final: 0.5230 (pm20) REVERT: D 143 SER cc_start: 0.6701 (m) cc_final: 0.6403 (p) REVERT: D 194 LYS cc_start: 0.5272 (OUTLIER) cc_final: 0.4813 (mmtm) REVERT: D 250 GLU cc_start: 0.6829 (tt0) cc_final: 0.6294 (mm-30) REVERT: D 260 LYS cc_start: 0.6628 (ttmm) cc_final: 0.5812 (ttpp) REVERT: D 264 GLN cc_start: 0.6564 (tt0) cc_final: 0.6043 (mt0) REVERT: D 280 GLN cc_start: 0.7109 (mm-40) cc_final: 0.6832 (mm-40) outliers start: 28 outliers final: 16 residues processed: 141 average time/residue: 1.4841 time to fit residues: 221.9342 Evaluate side-chains 138 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 194 LYS Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 333 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 8.9990 chunk 121 optimal weight: 0.0570 chunk 71 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10216 Z= 0.236 Angle : 0.697 9.218 13848 Z= 0.390 Chirality : 0.051 0.222 1576 Planarity : 0.007 0.068 1796 Dihedral : 5.166 18.708 1412 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.27 % Allowed : 13.73 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.24), residues: 1328 helix: 1.30 (0.26), residues: 392 sheet: -0.28 (0.40), residues: 176 loop : -0.13 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 87 HIS 0.004 0.001 HIS C 53 PHE 0.017 0.002 PHE C 233 TYR 0.016 0.002 TYR B 314 ARG 0.003 0.001 ARG B 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 1.105 Fit side-chains REVERT: A 29 ASP cc_start: 0.6914 (m-30) cc_final: 0.6630 (m-30) REVERT: A 113 GLN cc_start: 0.5959 (OUTLIER) cc_final: 0.5734 (mt0) REVERT: A 138 GLU cc_start: 0.6841 (mm-30) cc_final: 0.5258 (pm20) REVERT: A 143 SER cc_start: 0.6710 (m) cc_final: 0.6404 (p) REVERT: A 194 LYS cc_start: 0.5323 (OUTLIER) cc_final: 0.4872 (mmtm) REVERT: A 250 GLU cc_start: 0.6842 (tt0) cc_final: 0.6096 (mt-10) REVERT: A 260 LYS cc_start: 0.6626 (ttmm) cc_final: 0.5816 (ttpp) REVERT: A 264 GLN cc_start: 0.6446 (tt0) cc_final: 0.5919 (mt0) REVERT: A 280 GLN cc_start: 0.7188 (mm-40) cc_final: 0.6906 (mm-40) REVERT: B 29 ASP cc_start: 0.6914 (m-30) cc_final: 0.6631 (m-30) REVERT: B 113 GLN cc_start: 0.5959 (OUTLIER) cc_final: 0.5733 (mt0) REVERT: B 138 GLU cc_start: 0.6843 (mm-30) cc_final: 0.5259 (pm20) REVERT: B 143 SER cc_start: 0.6707 (m) cc_final: 0.6408 (p) REVERT: B 145 LYS cc_start: 0.7522 (mtmt) cc_final: 0.7034 (mmtt) REVERT: B 194 LYS cc_start: 0.5322 (OUTLIER) cc_final: 0.4870 (mmtm) REVERT: B 250 GLU cc_start: 0.6837 (tt0) cc_final: 0.6298 (mm-30) REVERT: B 260 LYS cc_start: 0.6625 (ttmm) cc_final: 0.5816 (ttpp) REVERT: B 264 GLN cc_start: 0.6445 (tt0) cc_final: 0.5918 (mt0) REVERT: B 280 GLN cc_start: 0.7197 (mm-40) cc_final: 0.6917 (mm-40) REVERT: C 29 ASP cc_start: 0.6915 (m-30) cc_final: 0.6631 (m-30) REVERT: C 113 GLN cc_start: 0.5959 (OUTLIER) cc_final: 0.5733 (mt0) REVERT: C 138 GLU cc_start: 0.6842 (mm-30) cc_final: 0.5260 (pm20) REVERT: C 143 SER cc_start: 0.6711 (m) cc_final: 0.6406 (p) REVERT: C 194 LYS cc_start: 0.5324 (OUTLIER) cc_final: 0.4872 (mmtm) REVERT: C 250 GLU cc_start: 0.6843 (tt0) cc_final: 0.6302 (mm-30) REVERT: C 260 LYS cc_start: 0.6623 (ttmm) cc_final: 0.5815 (ttpp) REVERT: C 264 GLN cc_start: 0.6445 (tt0) cc_final: 0.5919 (mt0) REVERT: C 280 GLN cc_start: 0.7194 (mm-40) cc_final: 0.6914 (mm-40) REVERT: D 29 ASP cc_start: 0.6913 (m-30) cc_final: 0.6631 (m-30) REVERT: D 113 GLN cc_start: 0.5958 (OUTLIER) cc_final: 0.5732 (mt0) REVERT: D 138 GLU cc_start: 0.6842 (mm-30) cc_final: 0.5261 (pm20) REVERT: D 143 SER cc_start: 0.6712 (m) cc_final: 0.6405 (p) REVERT: D 194 LYS cc_start: 0.5320 (OUTLIER) cc_final: 0.4869 (mmtm) REVERT: D 250 GLU cc_start: 0.6842 (tt0) cc_final: 0.6300 (mm-30) REVERT: D 260 LYS cc_start: 0.6624 (ttmm) cc_final: 0.5815 (ttpp) REVERT: D 264 GLN cc_start: 0.6455 (tt0) cc_final: 0.5930 (mt0) REVERT: D 280 GLN cc_start: 0.7196 (mm-40) cc_final: 0.6916 (mm-40) outliers start: 24 outliers final: 16 residues processed: 137 average time/residue: 1.4340 time to fit residues: 208.8360 Evaluate side-chains 141 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 194 LYS Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 333 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.0270 chunk 87 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10216 Z= 0.224 Angle : 0.678 9.015 13848 Z= 0.380 Chirality : 0.050 0.210 1576 Planarity : 0.006 0.070 1796 Dihedral : 5.144 19.063 1412 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.27 % Allowed : 13.73 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.24), residues: 1328 helix: 1.34 (0.26), residues: 392 sheet: -0.28 (0.39), residues: 176 loop : -0.13 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 87 HIS 0.004 0.001 HIS A 53 PHE 0.016 0.002 PHE D 233 TYR 0.015 0.002 TYR D 314 ARG 0.002 0.000 ARG D 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 1.147 Fit side-chains REVERT: A 29 ASP cc_start: 0.6909 (m-30) cc_final: 0.6626 (m-30) REVERT: A 113 GLN cc_start: 0.5958 (OUTLIER) cc_final: 0.5733 (mt0) REVERT: A 138 GLU cc_start: 0.6840 (mm-30) cc_final: 0.5255 (pm20) REVERT: A 143 SER cc_start: 0.6703 (m) cc_final: 0.6399 (p) REVERT: A 194 LYS cc_start: 0.5321 (OUTLIER) cc_final: 0.4871 (mmtm) REVERT: A 250 GLU cc_start: 0.6844 (tt0) cc_final: 0.6095 (mt-10) REVERT: A 260 LYS cc_start: 0.6623 (ttmm) cc_final: 0.5814 (ttpp) REVERT: A 264 GLN cc_start: 0.6464 (tt0) cc_final: 0.5941 (mt0) REVERT: A 280 GLN cc_start: 0.7182 (mm-40) cc_final: 0.6902 (mm-40) REVERT: B 29 ASP cc_start: 0.6909 (m-30) cc_final: 0.6628 (m-30) REVERT: B 113 GLN cc_start: 0.5958 (OUTLIER) cc_final: 0.5732 (mt0) REVERT: B 138 GLU cc_start: 0.6842 (mm-30) cc_final: 0.5257 (pm20) REVERT: B 143 SER cc_start: 0.6744 (m) cc_final: 0.6427 (p) REVERT: B 145 LYS cc_start: 0.7556 (mtmt) cc_final: 0.7060 (mmtt) REVERT: B 194 LYS cc_start: 0.5265 (OUTLIER) cc_final: 0.4807 (mmtm) REVERT: B 250 GLU cc_start: 0.6837 (tt0) cc_final: 0.6304 (mm-30) REVERT: B 260 LYS cc_start: 0.6622 (ttmm) cc_final: 0.5813 (ttpp) REVERT: B 264 GLN cc_start: 0.6548 (tt0) cc_final: 0.6032 (mt0) REVERT: B 280 GLN cc_start: 0.7182 (mm-40) cc_final: 0.6902 (mm-40) REVERT: C 29 ASP cc_start: 0.6911 (m-30) cc_final: 0.6625 (m-30) REVERT: C 113 GLN cc_start: 0.5959 (OUTLIER) cc_final: 0.5732 (mt0) REVERT: C 138 GLU cc_start: 0.6842 (mm-30) cc_final: 0.5257 (pm20) REVERT: C 143 SER cc_start: 0.6716 (m) cc_final: 0.6408 (p) REVERT: C 194 LYS cc_start: 0.5321 (OUTLIER) cc_final: 0.4870 (mmtm) REVERT: C 250 GLU cc_start: 0.6844 (tt0) cc_final: 0.6308 (mm-30) REVERT: C 260 LYS cc_start: 0.6621 (ttmm) cc_final: 0.5813 (ttpp) REVERT: C 264 GLN cc_start: 0.6547 (tt0) cc_final: 0.6033 (mt0) REVERT: C 280 GLN cc_start: 0.7181 (mm-40) cc_final: 0.6901 (mm-40) REVERT: D 29 ASP cc_start: 0.6909 (m-30) cc_final: 0.6624 (m-30) REVERT: D 113 GLN cc_start: 0.5958 (OUTLIER) cc_final: 0.5732 (mt0) REVERT: D 138 GLU cc_start: 0.6840 (mm-30) cc_final: 0.5257 (pm20) REVERT: D 143 SER cc_start: 0.6718 (m) cc_final: 0.6410 (p) REVERT: D 194 LYS cc_start: 0.5264 (OUTLIER) cc_final: 0.4807 (mmtm) REVERT: D 250 GLU cc_start: 0.6843 (tt0) cc_final: 0.6306 (mm-30) REVERT: D 260 LYS cc_start: 0.6621 (ttmm) cc_final: 0.5813 (ttpp) REVERT: D 264 GLN cc_start: 0.6549 (tt0) cc_final: 0.6031 (mt0) REVERT: D 280 GLN cc_start: 0.7181 (mm-40) cc_final: 0.6901 (mm-40) outliers start: 24 outliers final: 16 residues processed: 137 average time/residue: 1.4442 time to fit residues: 210.2638 Evaluate side-chains 141 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 194 LYS Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 333 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 0.2980 chunk 104 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.151933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.133197 restraints weight = 7109.310| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 0.63 r_work: 0.3305 rms_B_bonded: 1.12 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 1.90 restraints_weight: 0.2500 r_work: 0.3050 rms_B_bonded: 4.92 restraints_weight: 0.1250 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 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 : 0.003 0.024 10216 Z= 0.204 Angle : 0.653 8.686 13848 Z= 0.365 Chirality : 0.049 0.200 1576 Planarity : 0.006 0.070 1796 Dihedral : 5.099 19.284 1412 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.18 % Allowed : 13.83 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.24), residues: 1328 helix: 1.40 (0.26), residues: 392 sheet: -0.21 (0.40), residues: 176 loop : -0.12 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 87 HIS 0.004 0.001 HIS B 53 PHE 0.016 0.002 PHE B 233 TYR 0.015 0.002 TYR D 314 ARG 0.002 0.000 ARG D 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4153.59 seconds wall clock time: 73 minutes 43.94 seconds (4423.94 seconds total)