Starting phenix.real_space_refine on Mon Aug 5 05:22:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twv_41672/08_2024/8twv_41672.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twv_41672/08_2024/8twv_41672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twv_41672/08_2024/8twv_41672.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twv_41672/08_2024/8twv_41672.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twv_41672/08_2024/8twv_41672.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twv_41672/08_2024/8twv_41672.cif" } resolution = 3.4 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= 0.009 sd= 0.220 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 25 5.16 5 C 8305 2.51 5 N 2115 2.21 5 O 2275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 30": "OE1" <-> "OE2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "C GLU 30": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 12720 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2540 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain: "E" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2540 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain: "B" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2540 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain: "D" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2540 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain: "C" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2540 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.61, per 1000 atoms: 0.68 Number of scatterers: 12720 At special positions: 0 Unit cell: (92.352, 91.168, 124.32, 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 25 16.00 O 2275 8.00 N 2115 7.00 C 8305 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: 4.88 Conformation dependent library (CDL) restraints added in 2.2 seconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2930 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 15 sheets defined 34.2% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 62 through 70 removed outlier: 3.678A pdb=" N TRP A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 208 through 221 Processing helix chain 'A' and resid 227 through 245 removed outlier: 3.961A pdb=" N THR A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.718A pdb=" N ILE A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 287 Processing helix chain 'A' and resid 299 through 320 removed outlier: 3.618A pdb=" N ALA A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) Proline residue: A 305 - end of helix removed outlier: 3.505A pdb=" N GLY A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 315 " --> pdb=" O ILE A 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 70 removed outlier: 3.678A pdb=" N TRP E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 208 Processing helix chain 'E' and resid 208 through 221 Processing helix chain 'E' and resid 227 through 245 removed outlier: 3.961A pdb=" N THR E 234 " --> pdb=" O GLU E 230 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER E 235 " --> pdb=" O ARG E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 253 removed outlier: 3.718A pdb=" N ILE E 252 " --> pdb=" O TYR E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 287 Processing helix chain 'E' and resid 299 through 320 removed outlier: 3.617A pdb=" N ALA E 303 " --> pdb=" O ARG E 299 " (cutoff:3.500A) Proline residue: E 305 - end of helix removed outlier: 3.506A pdb=" N GLY E 312 " --> pdb=" O PHE E 308 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU E 315 " --> pdb=" O ILE E 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 70 removed outlier: 3.678A pdb=" N TRP B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 208 Processing helix chain 'B' and resid 208 through 221 Processing helix chain 'B' and resid 227 through 245 removed outlier: 3.961A pdb=" N THR B 234 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER B 235 " --> pdb=" O ARG B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.718A pdb=" N ILE B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 287 Processing helix chain 'B' and resid 299 through 320 removed outlier: 3.618A pdb=" N ALA B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) Proline residue: B 305 - end of helix removed outlier: 3.505A pdb=" N GLY B 312 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 315 " --> pdb=" O ILE B 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 70 removed outlier: 3.679A pdb=" N TRP D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 208 through 221 Processing helix chain 'D' and resid 227 through 245 removed outlier: 3.960A pdb=" N THR D 234 " --> pdb=" O GLU D 230 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 253 removed outlier: 3.717A pdb=" N ILE D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 287 Processing helix chain 'D' and resid 299 through 320 removed outlier: 3.618A pdb=" N ALA D 303 " --> pdb=" O ARG D 299 " (cutoff:3.500A) Proline residue: D 305 - end of helix removed outlier: 3.505A pdb=" N GLY D 312 " --> pdb=" O PHE D 308 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 315 " --> pdb=" O ILE D 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 70 removed outlier: 3.679A pdb=" N TRP C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 227 through 245 removed outlier: 3.961A pdb=" N THR C 234 " --> pdb=" O GLU C 230 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C 235 " --> pdb=" O ARG C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 253 removed outlier: 3.717A pdb=" N ILE C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 287 Processing helix chain 'C' and resid 299 through 320 removed outlier: 3.618A pdb=" N ALA C 303 " --> pdb=" O ARG C 299 " (cutoff:3.500A) Proline residue: C 305 - end of helix removed outlier: 3.505A pdb=" N GLY C 312 " --> pdb=" O PHE C 308 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 315 " --> pdb=" O ILE C 311 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 removed outlier: 4.475A pdb=" N SER A 109 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58 removed outlier: 4.056A pdb=" N LYS A 34 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N GLY A 25 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ASP A 36 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE A 23 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N TYR A 38 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN A 21 " --> pdb=" O TYR A 38 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL A 40 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N PHE A 19 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLN A 42 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N SER A 17 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N THR A 44 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N SER A 15 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL A 16 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE A 145 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE A 18 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL A 147 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE A 20 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.511A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE A 188 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER A 171 " --> pdb=" O PHE A 188 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG A 190 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N HIS A 169 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR A 192 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N SER A 167 " --> pdb=" O THR A 192 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ARG A 194 " --> pdb=" O LYS A 165 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LYS A 165 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASP A 196 " --> pdb=" O ARG A 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 56 through 58 removed outlier: 4.475A pdb=" N SER E 109 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 56 through 58 removed outlier: 4.056A pdb=" N LYS E 34 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N GLY E 25 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASP E 36 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE E 23 " --> pdb=" O ASP E 36 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N TYR E 38 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN E 21 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL E 40 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N PHE E 19 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLN E 42 " --> pdb=" O SER E 17 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N SER E 17 " --> pdb=" O GLN E 42 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N THR E 44 " --> pdb=" O SER E 15 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N SER E 15 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL E 16 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE E 145 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE E 18 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL E 147 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE E 20 " --> pdb=" O VAL E 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.512A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE E 188 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER E 171 " --> pdb=" O PHE E 188 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG E 190 " --> pdb=" O HIS E 169 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N HIS E 169 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR E 192 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N SER E 167 " --> pdb=" O THR E 192 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ARG E 194 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LYS E 165 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASP E 196 " --> pdb=" O ARG E 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 56 through 58 removed outlier: 4.475A pdb=" N SER B 109 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 56 through 58 removed outlier: 4.055A pdb=" N LYS B 34 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N GLY B 25 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ASP B 36 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE B 23 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N TYR B 38 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN B 21 " --> pdb=" O TYR B 38 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL B 40 " --> pdb=" O PHE B 19 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N PHE B 19 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLN B 42 " --> pdb=" O SER B 17 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N SER B 17 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N THR B 44 " --> pdb=" O SER B 15 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N SER B 15 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL B 16 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE B 145 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE B 18 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL B 147 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE B 20 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.511A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE B 188 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER B 171 " --> pdb=" O PHE B 188 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG B 190 " --> pdb=" O HIS B 169 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N HIS B 169 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR B 192 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N SER B 167 " --> pdb=" O THR B 192 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ARG B 194 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LYS B 165 " --> pdb=" O ARG B 194 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASP B 196 " --> pdb=" O ARG B 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 56 through 58 removed outlier: 4.475A pdb=" N SER D 109 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 56 through 58 removed outlier: 4.056A pdb=" N LYS D 34 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N GLY D 25 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASP D 36 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE D 23 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N TYR D 38 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASN D 21 " --> pdb=" O TYR D 38 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL D 40 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N PHE D 19 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N GLN D 42 " --> pdb=" O SER D 17 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N SER D 17 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N THR D 44 " --> pdb=" O SER D 15 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N SER D 15 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL D 16 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE D 145 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE D 18 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL D 147 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE D 20 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.512A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE D 188 " --> pdb=" O SER D 171 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER D 171 " --> pdb=" O PHE D 188 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG D 190 " --> pdb=" O HIS D 169 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N HIS D 169 " --> pdb=" O ARG D 190 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR D 192 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N SER D 167 " --> pdb=" O THR D 192 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ARG D 194 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LYS D 165 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASP D 196 " --> pdb=" O ARG D 163 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 56 through 58 removed outlier: 4.476A pdb=" N SER C 109 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 56 through 58 removed outlier: 4.056A pdb=" N LYS C 34 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N GLY C 25 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ASP C 36 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE C 23 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N TYR C 38 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN C 21 " --> pdb=" O TYR C 38 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL C 40 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N PHE C 19 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLN C 42 " --> pdb=" O SER C 17 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N SER C 17 " --> pdb=" O GLN C 42 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N THR C 44 " --> pdb=" O SER C 15 " (cutoff:3.500A) removed outlier: 9.610A pdb=" N SER C 15 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL C 16 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE C 145 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE C 18 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL C 147 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE C 20 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.512A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE C 188 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER C 171 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG C 190 " --> pdb=" O HIS C 169 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N HIS C 169 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR C 192 " --> pdb=" O SER C 167 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N SER C 167 " --> pdb=" O THR C 192 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ARG C 194 " --> pdb=" O LYS C 165 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LYS C 165 " --> pdb=" O ARG C 194 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASP C 196 " --> pdb=" O ARG C 163 " (cutoff:3.500A) 575 hydrogen bonds defined for protein. 1680 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: 3.79 Time building geometry restraints manager: 5.41 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: 4020 1.34 - 1.46: 2849 1.46 - 1.57: 6146 1.57 - 1.69: 5 1.69 - 1.81: 45 Bond restraints: 13065 Sorted by residual: bond pdb=" CA PHE B 208 " pdb=" CB PHE B 208 " ideal model delta sigma weight residual 1.530 1.560 -0.030 1.69e-02 3.50e+03 3.10e+00 bond pdb=" CA PHE A 208 " pdb=" CB PHE A 208 " ideal model delta sigma weight residual 1.530 1.560 -0.030 1.69e-02 3.50e+03 3.07e+00 bond pdb=" CA PHE E 208 " pdb=" CB PHE E 208 " ideal model delta sigma weight residual 1.530 1.560 -0.030 1.69e-02 3.50e+03 3.06e+00 bond pdb=" CA PHE C 208 " pdb=" CB PHE C 208 " ideal model delta sigma weight residual 1.530 1.560 -0.029 1.69e-02 3.50e+03 3.02e+00 bond pdb=" CA PHE D 208 " pdb=" CB PHE D 208 " ideal model delta sigma weight residual 1.530 1.560 -0.029 1.69e-02 3.50e+03 3.01e+00 ... (remaining 13060 not shown) Histogram of bond angle deviations from ideal: 98.88 - 105.94: 280 105.94 - 112.99: 6777 112.99 - 120.04: 4668 120.04 - 127.09: 5881 127.09 - 134.15: 174 Bond angle restraints: 17780 Sorted by residual: angle pdb=" N ARG D 299 " pdb=" CA ARG D 299 " pdb=" C ARG D 299 " ideal model delta sigma weight residual 113.20 107.78 5.42 1.21e+00 6.83e-01 2.01e+01 angle pdb=" N ARG B 299 " pdb=" CA ARG B 299 " pdb=" C ARG B 299 " ideal model delta sigma weight residual 113.20 107.81 5.39 1.21e+00 6.83e-01 1.99e+01 angle pdb=" N ARG A 299 " pdb=" CA ARG A 299 " pdb=" C ARG A 299 " ideal model delta sigma weight residual 113.20 107.82 5.38 1.21e+00 6.83e-01 1.98e+01 angle pdb=" N ARG C 299 " pdb=" CA ARG C 299 " pdb=" C ARG C 299 " ideal model delta sigma weight residual 113.20 107.83 5.37 1.21e+00 6.83e-01 1.97e+01 angle pdb=" N ARG E 299 " pdb=" CA ARG E 299 " pdb=" C ARG E 299 " ideal model delta sigma weight residual 113.20 107.86 5.34 1.21e+00 6.83e-01 1.95e+01 ... (remaining 17775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 6675 17.64 - 35.27: 696 35.27 - 52.91: 179 52.91 - 70.55: 45 70.55 - 88.19: 10 Dihedral angle restraints: 7605 sinusoidal: 3060 harmonic: 4545 Sorted by residual: dihedral pdb=" CA ASP D 115 " pdb=" CB ASP D 115 " pdb=" CG ASP D 115 " pdb=" OD1 ASP D 115 " ideal model delta sinusoidal sigma weight residual -30.00 -88.59 58.59 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP B 115 " pdb=" CB ASP B 115 " pdb=" CG ASP B 115 " pdb=" OD1 ASP B 115 " ideal model delta sinusoidal sigma weight residual -30.00 -88.58 58.58 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP E 115 " pdb=" CB ASP E 115 " pdb=" CG ASP E 115 " pdb=" OD1 ASP E 115 " ideal model delta sinusoidal sigma weight residual -30.00 -88.56 58.56 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 7602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1255 0.042 - 0.083: 446 0.083 - 0.125: 201 0.125 - 0.166: 38 0.166 - 0.208: 15 Chirality restraints: 1955 Sorted by residual: chirality pdb=" CA THR A 61 " pdb=" N THR A 61 " pdb=" C THR A 61 " pdb=" CB THR A 61 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA THR C 61 " pdb=" N THR C 61 " pdb=" C THR C 61 " pdb=" CB THR C 61 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA THR D 61 " pdb=" N THR D 61 " pdb=" C THR D 61 " pdb=" CB THR D 61 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1952 not shown) Planarity restraints: 2265 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 208 " 0.011 2.00e-02 2.50e+03 1.79e-02 5.63e+00 pdb=" CG PHE C 208 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE C 208 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE C 208 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE C 208 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 208 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 208 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 208 " 0.011 2.00e-02 2.50e+03 1.79e-02 5.62e+00 pdb=" CG PHE B 208 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE B 208 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 208 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE B 208 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 208 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 208 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 208 " 0.011 2.00e-02 2.50e+03 1.79e-02 5.59e+00 pdb=" CG PHE E 208 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE E 208 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE E 208 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE E 208 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 208 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE E 208 " -0.000 2.00e-02 2.50e+03 ... (remaining 2262 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 2493 2.78 - 3.31: 11409 3.31 - 3.84: 21313 3.84 - 4.37: 25170 4.37 - 4.90: 43579 Nonbonded interactions: 103964 Sorted by model distance: nonbonded pdb=" OE2 GLU D 59 " pdb=" OG SER C 134 " model vdw 2.244 3.040 nonbonded pdb=" OE2 GLU E 59 " pdb=" OG SER D 134 " model vdw 2.256 3.040 nonbonded pdb=" O THR E 61 " pdb=" OG1 THR E 61 " model vdw 2.303 3.040 nonbonded pdb=" O THR A 61 " pdb=" OG1 THR A 61 " model vdw 2.304 3.040 nonbonded pdb=" O THR B 61 " pdb=" OG1 THR B 61 " model vdw 2.304 3.040 ... (remaining 103959 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 37.430 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 0.054 13065 Z= 0.266 Angle : 0.727 8.046 17780 Z= 0.437 Chirality : 0.053 0.208 1955 Planarity : 0.005 0.062 2265 Dihedral : 15.797 88.185 4675 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.07 % Allowed : 19.13 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.21), residues: 1540 helix: -1.61 (0.19), residues: 525 sheet: 1.36 (0.27), residues: 430 loop : -2.25 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 206 HIS 0.006 0.001 HIS A 285 PHE 0.040 0.002 PHE B 208 TYR 0.009 0.001 TYR B 38 ARG 0.010 0.001 ARG B 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ARG cc_start: 0.6869 (mtm180) cc_final: 0.6411 (mpt-90) REVERT: E 34 LYS cc_start: 0.8971 (mttp) cc_final: 0.8762 (mttm) REVERT: E 208 PHE cc_start: 0.8704 (t80) cc_final: 0.8396 (t80) REVERT: E 230 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6983 (mp0) REVERT: E 231 ARG cc_start: 0.6850 (mtm180) cc_final: 0.6450 (mpt-90) REVERT: B 225 LEU cc_start: 0.8615 (mp) cc_final: 0.8385 (mp) REVERT: B 231 ARG cc_start: 0.6871 (mtm180) cc_final: 0.6335 (mpt-90) REVERT: D 86 ASP cc_start: 0.8750 (t70) cc_final: 0.8482 (t70) REVERT: D 230 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7121 (mp0) REVERT: D 231 ARG cc_start: 0.6980 (mtm180) cc_final: 0.6661 (mpt-90) REVERT: C 113 ASP cc_start: 0.8233 (m-30) cc_final: 0.7625 (p0) REVERT: C 208 PHE cc_start: 0.8676 (t80) cc_final: 0.8473 (t80) REVERT: C 231 ARG cc_start: 0.6807 (mtm180) cc_final: 0.6369 (mpt-90) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.2583 time to fit residues: 53.9690 Evaluate side-chains 116 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 65 optimal weight: 0.0270 chunk 40 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 overall best weight: 1.7642 ------------------------------------------------------------------------------- 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: 0.8126 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 13065 Z= 0.260 Angle : 0.549 7.273 17780 Z= 0.280 Chirality : 0.046 0.133 1955 Planarity : 0.003 0.022 2265 Dihedral : 4.293 14.832 1715 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.45 % Allowed : 18.84 % Favored : 78.70 % 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: -0.22 (0.22), residues: 1540 helix: 0.54 (0.24), residues: 505 sheet: 1.06 (0.25), residues: 480 loop : -1.92 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 206 HIS 0.004 0.001 HIS A 285 PHE 0.011 0.001 PHE A 208 TYR 0.011 0.001 TYR D 33 ARG 0.003 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 124 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 LYS cc_start: 0.9045 (mttp) cc_final: 0.8802 (mttm) REVERT: E 231 ARG cc_start: 0.7131 (mtm180) cc_final: 0.6881 (mtt-85) REVERT: B 86 ASP cc_start: 0.8755 (t70) cc_final: 0.8305 (t70) REVERT: B 151 ASN cc_start: 0.8388 (OUTLIER) cc_final: 0.7817 (m110) REVERT: B 225 LEU cc_start: 0.8818 (mp) cc_final: 0.8544 (mp) REVERT: B 231 ARG cc_start: 0.6953 (mtm180) cc_final: 0.6127 (mpt-90) REVERT: D 30 GLU cc_start: 0.8802 (pm20) cc_final: 0.8121 (pm20) REVERT: D 151 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.7579 (t0) REVERT: D 231 ARG cc_start: 0.7094 (mtm180) cc_final: 0.6780 (mtt-85) REVERT: D 264 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8243 (mt0) REVERT: C 151 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8261 (t0) REVERT: C 185 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8648 (pt0) outliers start: 34 outliers final: 16 residues processed: 158 average time/residue: 0.2344 time to fit residues: 54.5180 Evaluate side-chains 136 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 185 GLN Chi-restraints excluded: chain C residue 214 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 141 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13065 Z= 0.201 Angle : 0.492 6.374 17780 Z= 0.250 Chirality : 0.045 0.128 1955 Planarity : 0.003 0.021 2265 Dihedral : 4.151 18.957 1715 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.88 % Allowed : 19.86 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.22), residues: 1540 helix: 1.06 (0.24), residues: 505 sheet: 1.01 (0.25), residues: 475 loop : -1.84 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 206 HIS 0.004 0.001 HIS A 285 PHE 0.007 0.001 PHE A 208 TYR 0.010 0.001 TYR D 38 ARG 0.003 0.000 ARG D 231 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8109 (m-30) cc_final: 0.7597 (p0) REVERT: A 264 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8240 (mt0) REVERT: E 231 ARG cc_start: 0.7131 (mtm180) cc_final: 0.6924 (mtt180) REVERT: E 264 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7609 (mt0) REVERT: B 34 LYS cc_start: 0.9011 (mttp) cc_final: 0.8700 (mttm) REVERT: B 86 ASP cc_start: 0.8771 (t70) cc_final: 0.8367 (t70) REVERT: D 231 ARG cc_start: 0.7077 (mtm180) cc_final: 0.6486 (mtt180) REVERT: C 239 MET cc_start: 0.8502 (ttt) cc_final: 0.8268 (ttt) outliers start: 26 outliers final: 14 residues processed: 145 average time/residue: 0.2471 time to fit residues: 52.3336 Evaluate side-chains 131 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 265 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 124 optimal weight: 0.0170 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN E 298 GLN B 298 GLN C 251 ASN C 298 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13065 Z= 0.282 Angle : 0.522 7.385 17780 Z= 0.267 Chirality : 0.046 0.131 1955 Planarity : 0.003 0.019 2265 Dihedral : 4.307 18.715 1715 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.54 % Allowed : 17.55 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.22), residues: 1540 helix: 1.26 (0.24), residues: 505 sheet: 1.11 (0.25), residues: 470 loop : -1.76 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 206 HIS 0.004 0.001 HIS A 285 PHE 0.008 0.001 PHE C 133 TYR 0.011 0.001 TYR C 204 ARG 0.002 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 131 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8028 (mmm-85) cc_final: 0.7778 (tpp80) REVERT: A 129 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8425 (mt-10) REVERT: A 161 TRP cc_start: 0.8272 (m-10) cc_final: 0.7531 (m-90) REVERT: A 264 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8337 (mt0) REVERT: E 264 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8366 (mt0) REVERT: B 86 ASP cc_start: 0.8805 (t70) cc_final: 0.8411 (t70) REVERT: B 129 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8190 (mt-10) REVERT: B 151 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.7970 (m110) REVERT: D 30 GLU cc_start: 0.8879 (pm20) cc_final: 0.8553 (pm20) REVERT: D 151 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8037 (m110) REVERT: D 245 TYR cc_start: 0.7751 (m-10) cc_final: 0.7429 (m-80) REVERT: D 264 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8266 (mt0) REVERT: C 151 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8377 (t0) REVERT: C 185 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8608 (pt0) REVERT: C 239 MET cc_start: 0.8580 (ttt) cc_final: 0.8313 (ttt) outliers start: 49 outliers final: 31 residues processed: 175 average time/residue: 0.2354 time to fit residues: 60.1950 Evaluate side-chains 165 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 125 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 185 GLN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 265 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 61 optimal weight: 0.0570 chunk 127 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 0.3980 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN D 298 GLN C 251 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 13065 Z= 0.141 Angle : 0.462 5.709 17780 Z= 0.234 Chirality : 0.044 0.126 1955 Planarity : 0.002 0.022 2265 Dihedral : 3.966 15.421 1715 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.73 % Allowed : 19.35 % Favored : 78.92 % 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: 0.31 (0.22), residues: 1540 helix: 1.43 (0.24), residues: 505 sheet: 1.13 (0.26), residues: 455 loop : -1.74 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 206 HIS 0.004 0.001 HIS A 285 PHE 0.006 0.001 PHE C 228 TYR 0.009 0.001 TYR D 38 ARG 0.002 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8234 (mt0) REVERT: B 86 ASP cc_start: 0.8776 (t70) cc_final: 0.8472 (t70) REVERT: B 129 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8032 (mt-10) REVERT: B 231 ARG cc_start: 0.7365 (mtm180) cc_final: 0.6684 (mtt-85) REVERT: D 231 ARG cc_start: 0.7119 (mtm180) cc_final: 0.6651 (mtm-85) REVERT: D 248 TYR cc_start: 0.9001 (t80) cc_final: 0.8771 (t80) REVERT: C 239 MET cc_start: 0.8572 (ttt) cc_final: 0.8280 (ttt) outliers start: 24 outliers final: 17 residues processed: 147 average time/residue: 0.2368 time to fit residues: 51.2438 Evaluate side-chains 134 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain C residue 60 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN C 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13065 Z= 0.372 Angle : 0.549 7.211 17780 Z= 0.281 Chirality : 0.047 0.138 1955 Planarity : 0.003 0.020 2265 Dihedral : 4.313 20.331 1715 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.32 % Allowed : 18.48 % Favored : 78.19 % 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: 0.28 (0.22), residues: 1540 helix: 1.38 (0.24), residues: 505 sheet: 1.22 (0.26), residues: 450 loop : -1.81 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 206 HIS 0.003 0.001 HIS A 285 PHE 0.009 0.001 PHE D 133 TYR 0.012 0.002 TYR C 204 ARG 0.002 0.000 ARG D 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 128 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8057 (mmm-85) cc_final: 0.7810 (tpp80) REVERT: A 129 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8453 (mt-10) REVERT: A 161 TRP cc_start: 0.8285 (m-10) cc_final: 0.7536 (m-90) REVERT: A 264 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8429 (mt0) REVERT: E 231 ARG cc_start: 0.7478 (mtm180) cc_final: 0.7038 (mtt180) REVERT: E 264 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8473 (mt0) REVERT: B 30 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: B 129 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8371 (mt-10) REVERT: B 169 HIS cc_start: 0.7656 (t70) cc_final: 0.7406 (t70) REVERT: B 232 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7517 (mp) REVERT: D 30 GLU cc_start: 0.8931 (pm20) cc_final: 0.8603 (pm20) REVERT: D 129 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8289 (mt-10) REVERT: D 231 ARG cc_start: 0.7153 (mtm180) cc_final: 0.6857 (mtm-85) REVERT: C 30 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8395 (pm20) REVERT: C 184 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.8135 (m-40) REVERT: C 239 MET cc_start: 0.8611 (ttt) cc_final: 0.8364 (ttt) outliers start: 46 outliers final: 32 residues processed: 169 average time/residue: 0.2373 time to fit residues: 59.0215 Evaluate side-chains 164 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 123 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 265 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 91 optimal weight: 0.3980 chunk 68 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN C 251 ASN C 264 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13065 Z= 0.247 Angle : 0.509 7.036 17780 Z= 0.257 Chirality : 0.045 0.128 1955 Planarity : 0.003 0.020 2265 Dihedral : 4.165 17.144 1715 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.54 % Allowed : 18.99 % Favored : 77.47 % 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: 0.28 (0.22), residues: 1540 helix: 1.41 (0.24), residues: 505 sheet: 1.20 (0.26), residues: 450 loop : -1.83 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 161 HIS 0.004 0.001 HIS A 285 PHE 0.007 0.001 PHE D 133 TYR 0.011 0.001 TYR D 204 ARG 0.002 0.000 ARG D 231 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 122 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.7784 (tpp80) REVERT: A 113 ASP cc_start: 0.8191 (m-30) cc_final: 0.7788 (p0) REVERT: A 129 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8400 (mt-10) REVERT: A 264 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8305 (mt0) REVERT: A 304 PHE cc_start: 0.4931 (OUTLIER) cc_final: 0.4294 (t80) REVERT: E 30 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8465 (pm20) REVERT: E 231 ARG cc_start: 0.7475 (mtm180) cc_final: 0.7054 (mtt180) REVERT: E 304 PHE cc_start: 0.4921 (OUTLIER) cc_final: 0.3719 (t80) REVERT: B 30 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8490 (pm20) REVERT: B 34 LYS cc_start: 0.9085 (mttp) cc_final: 0.8800 (mttm) REVERT: B 129 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8192 (mt-10) REVERT: B 304 PHE cc_start: 0.5138 (OUTLIER) cc_final: 0.4296 (t80) REVERT: D 30 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8541 (pm20) REVERT: D 129 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8253 (mt-10) REVERT: D 231 ARG cc_start: 0.7112 (mtm180) cc_final: 0.6850 (mtm-85) REVERT: D 304 PHE cc_start: 0.4913 (OUTLIER) cc_final: 0.3963 (t80) REVERT: C 30 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8444 (pm20) REVERT: C 151 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8343 (t0) REVERT: C 239 MET cc_start: 0.8597 (ttt) cc_final: 0.8330 (ttt) REVERT: C 304 PHE cc_start: 0.5314 (OUTLIER) cc_final: 0.4370 (t80) outliers start: 49 outliers final: 27 residues processed: 162 average time/residue: 0.2549 time to fit residues: 60.1343 Evaluate side-chains 158 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 117 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 304 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 304 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 0.0070 chunk 89 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN E 62 GLN B 62 GLN C 62 GLN C 251 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13065 Z= 0.172 Angle : 0.480 7.322 17780 Z= 0.241 Chirality : 0.044 0.126 1955 Planarity : 0.002 0.022 2265 Dihedral : 3.995 16.636 1715 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.47 % Allowed : 19.13 % Favored : 77.40 % 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: 0.30 (0.22), residues: 1540 helix: 1.49 (0.24), residues: 505 sheet: 1.09 (0.26), residues: 455 loop : -1.78 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 161 HIS 0.004 0.001 HIS A 285 PHE 0.006 0.001 PHE C 228 TYR 0.010 0.001 TYR D 38 ARG 0.002 0.000 ARG B 231 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 117 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8017 (mmm-85) cc_final: 0.7760 (tpp80) REVERT: A 113 ASP cc_start: 0.8188 (m-30) cc_final: 0.7791 (p0) REVERT: A 129 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8324 (mt-10) REVERT: A 264 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8172 (mt0) REVERT: A 304 PHE cc_start: 0.4891 (OUTLIER) cc_final: 0.4257 (t80) REVERT: E 30 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8430 (pm20) REVERT: E 304 PHE cc_start: 0.4936 (OUTLIER) cc_final: 0.3640 (t80) REVERT: B 30 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8281 (mp0) REVERT: B 34 LYS cc_start: 0.9070 (mttp) cc_final: 0.8774 (mttm) REVERT: B 129 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8032 (mt-10) REVERT: B 231 ARG cc_start: 0.7298 (mtm180) cc_final: 0.6699 (mtt-85) REVERT: B 304 PHE cc_start: 0.5252 (OUTLIER) cc_final: 0.4352 (t80) REVERT: D 30 GLU cc_start: 0.8813 (pm20) cc_final: 0.8487 (pm20) REVERT: D 65 ARG cc_start: 0.7740 (mmm-85) cc_final: 0.7355 (ttm-80) REVERT: D 231 ARG cc_start: 0.7068 (mtm180) cc_final: 0.6817 (mtm-85) REVERT: D 248 TYR cc_start: 0.9034 (t80) cc_final: 0.8770 (t80) REVERT: D 264 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8266 (mt0) REVERT: D 304 PHE cc_start: 0.4794 (OUTLIER) cc_final: 0.3834 (t80) REVERT: C 30 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8343 (pm20) REVERT: C 151 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.8149 (m110) REVERT: C 184 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.8171 (m-40) REVERT: C 239 MET cc_start: 0.8535 (ttt) cc_final: 0.8245 (ttt) REVERT: C 304 PHE cc_start: 0.5250 (OUTLIER) cc_final: 0.4340 (t80) outliers start: 48 outliers final: 27 residues processed: 160 average time/residue: 0.2462 time to fit residues: 57.0855 Evaluate side-chains 152 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 111 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 304 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 304 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 125 optimal weight: 0.0770 chunk 131 optimal weight: 0.0770 chunk 138 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 overall best weight: 1.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN E 154 ASN B 62 GLN B 154 ASN D 62 GLN C 62 GLN C 154 ASN C 251 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13065 Z= 0.197 Angle : 0.488 7.573 17780 Z= 0.247 Chirality : 0.045 0.126 1955 Planarity : 0.002 0.022 2265 Dihedral : 3.969 15.012 1715 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.68 % Allowed : 19.21 % Favored : 77.11 % 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: 0.28 (0.22), residues: 1540 helix: 1.49 (0.24), residues: 505 sheet: 1.07 (0.26), residues: 460 loop : -1.84 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 161 HIS 0.003 0.001 HIS D 285 PHE 0.006 0.001 PHE C 133 TYR 0.010 0.001 TYR D 38 ARG 0.002 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 114 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8018 (mmm-85) cc_final: 0.7767 (tpp80) REVERT: A 113 ASP cc_start: 0.8191 (m-30) cc_final: 0.7788 (p0) REVERT: A 129 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8339 (mt-10) REVERT: A 264 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8195 (mt0) REVERT: A 304 PHE cc_start: 0.4922 (OUTLIER) cc_final: 0.4250 (t80) REVERT: E 30 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8429 (pm20) REVERT: E 264 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8461 (mt0) REVERT: E 304 PHE cc_start: 0.4942 (OUTLIER) cc_final: 0.3656 (t80) REVERT: B 34 LYS cc_start: 0.9075 (mttp) cc_final: 0.8784 (mttm) REVERT: B 129 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8072 (mt-10) REVERT: B 231 ARG cc_start: 0.7324 (mtm180) cc_final: 0.6777 (mtt-85) REVERT: B 232 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7378 (mp) REVERT: B 304 PHE cc_start: 0.5092 (OUTLIER) cc_final: 0.4204 (t80) REVERT: D 30 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8520 (pm20) REVERT: D 65 ARG cc_start: 0.7676 (mmm-85) cc_final: 0.7285 (ttm-80) REVERT: D 231 ARG cc_start: 0.7094 (mtm180) cc_final: 0.6849 (mtm-85) REVERT: D 248 TYR cc_start: 0.9033 (t80) cc_final: 0.8820 (t80) REVERT: D 264 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8270 (mt0) REVERT: D 304 PHE cc_start: 0.4789 (OUTLIER) cc_final: 0.3834 (t80) REVERT: C 30 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8339 (pm20) REVERT: C 151 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.8169 (m110) REVERT: C 184 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.8134 (m-40) REVERT: C 230 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6668 (mp0) REVERT: C 239 MET cc_start: 0.8540 (ttt) cc_final: 0.8255 (ttt) REVERT: C 304 PHE cc_start: 0.5181 (OUTLIER) cc_final: 0.4320 (t80) outliers start: 51 outliers final: 30 residues processed: 157 average time/residue: 0.2453 time to fit residues: 56.0719 Evaluate side-chains 157 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 111 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 304 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 304 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 154 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 154 ASN B 154 ASN D 62 GLN D 154 ASN C 154 ASN C 251 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 13065 Z= 0.493 Angle : 0.612 7.826 17780 Z= 0.316 Chirality : 0.049 0.151 1955 Planarity : 0.003 0.019 2265 Dihedral : 4.554 23.330 1715 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.97 % Allowed : 18.84 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.22), residues: 1540 helix: 1.27 (0.24), residues: 500 sheet: 0.98 (0.26), residues: 455 loop : -1.89 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 161 HIS 0.003 0.001 HIS A 177 PHE 0.011 0.001 PHE E 208 TYR 0.016 0.002 TYR C 204 ARG 0.003 0.000 ARG E 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 123 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8032 (mmm-85) cc_final: 0.7687 (tpp80) REVERT: A 129 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8422 (mt-10) REVERT: A 264 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8417 (mt0) REVERT: A 304 PHE cc_start: 0.4995 (OUTLIER) cc_final: 0.4135 (t80) REVERT: E 30 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8482 (pm20) REVERT: E 231 ARG cc_start: 0.7451 (mtm180) cc_final: 0.7158 (mtt180) REVERT: E 264 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8462 (mt0) REVERT: E 304 PHE cc_start: 0.5159 (OUTLIER) cc_final: 0.4203 (t80) REVERT: B 30 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8516 (pm20) REVERT: B 69 ASN cc_start: 0.8737 (m-40) cc_final: 0.8528 (m-40) REVERT: B 129 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8390 (mt-10) REVERT: B 169 HIS cc_start: 0.7635 (t70) cc_final: 0.7370 (t70) REVERT: B 231 ARG cc_start: 0.7303 (mtm180) cc_final: 0.6889 (mtt180) REVERT: B 232 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7455 (mp) REVERT: B 304 PHE cc_start: 0.5226 (OUTLIER) cc_final: 0.4432 (t80) REVERT: D 30 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8627 (pm20) REVERT: D 129 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8292 (mt-10) REVERT: D 231 ARG cc_start: 0.7152 (mtm180) cc_final: 0.6914 (mtm-85) REVERT: D 264 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8401 (mt0) REVERT: D 304 PHE cc_start: 0.5024 (OUTLIER) cc_final: 0.3806 (t80) REVERT: C 30 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8471 (pm20) REVERT: C 151 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8236 (m-40) REVERT: C 184 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8180 (m-40) REVERT: C 239 MET cc_start: 0.8680 (ttt) cc_final: 0.8442 (ttt) REVERT: C 304 PHE cc_start: 0.5366 (OUTLIER) cc_final: 0.4489 (t80) outliers start: 55 outliers final: 32 residues processed: 169 average time/residue: 0.2397 time to fit residues: 59.1303 Evaluate side-chains 170 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 120 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 304 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 304 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN E 154 ASN B 154 ASN D 154 ASN D 251 ASN C 154 ASN C 251 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.129660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.096210 restraints weight = 16011.877| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.74 r_work: 0.3121 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13065 Z= 0.166 Angle : 0.490 8.012 17780 Z= 0.249 Chirality : 0.045 0.126 1955 Planarity : 0.002 0.021 2265 Dihedral : 4.079 14.612 1715 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.32 % Allowed : 19.71 % Favored : 76.97 % 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: 0.19 (0.22), residues: 1540 helix: 1.43 (0.24), residues: 505 sheet: 1.04 (0.26), residues: 450 loop : -1.87 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 161 HIS 0.004 0.001 HIS A 285 PHE 0.008 0.001 PHE B 208 TYR 0.010 0.001 TYR D 38 ARG 0.002 0.000 ARG A 286 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2398.53 seconds wall clock time: 43 minutes 28.24 seconds (2608.24 seconds total)