Starting phenix.real_space_refine on Sat Jul 20 23:44:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twv_41672/07_2024/8twv_41672.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twv_41672/07_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_41672/07_2024/8twv_41672.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twv_41672/07_2024/8twv_41672.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twv_41672/07_2024/8twv_41672.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twv_41672/07_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 7.58, per 1000 atoms: 0.60 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: 5.16 Conformation dependent library (CDL) restraints added in 2.0 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: 1.42 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: 3.48 Time building geometry restraints manager: 5.61 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 2.440 nonbonded pdb=" OE2 GLU E 59 " pdb=" OG SER D 134 " model vdw 2.256 2.440 nonbonded pdb=" O THR E 61 " pdb=" OG1 THR E 61 " model vdw 2.303 2.440 nonbonded pdb=" O THR A 61 " pdb=" OG1 THR A 61 " model vdw 2.304 2.440 nonbonded pdb=" O THR B 61 " pdb=" OG1 THR B 61 " model vdw 2.304 2.440 ... (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 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 35.560 Find NCS groups from input model: 0.710 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.350 ------------------------------------------------------------------------------- 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 : 1.601 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: 0.2657 time to fit residues: 55.7074 Evaluate side-chains 116 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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: 3.9990 chunk 117 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 79 optimal weight: 0.4980 chunk 62 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 chunk 47 optimal weight: 0.0980 chunk 73 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8063 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 13065 Z= 0.134 Angle : 0.484 7.217 17780 Z= 0.245 Chirality : 0.044 0.142 1955 Planarity : 0.003 0.022 2265 Dihedral : 4.032 15.846 1715 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.01 % Allowed : 20.22 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.22), residues: 1540 helix: 0.18 (0.23), residues: 535 sheet: 1.47 (0.27), residues: 425 loop : -2.00 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 206 HIS 0.004 0.001 HIS A 285 PHE 0.015 0.001 PHE A 208 TYR 0.012 0.001 TYR D 38 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 146 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ARG cc_start: 0.6856 (mtm180) cc_final: 0.6499 (mtt180) REVERT: E 34 LYS cc_start: 0.8941 (mttp) cc_final: 0.8700 (mttm) REVERT: E 231 ARG cc_start: 0.7019 (mtm180) cc_final: 0.6691 (mtt-85) REVERT: B 86 ASP cc_start: 0.8810 (t70) cc_final: 0.8423 (t70) REVERT: B 225 LEU cc_start: 0.8798 (mp) cc_final: 0.8478 (mp) REVERT: B 231 ARG cc_start: 0.6895 (mtm180) cc_final: 0.6070 (mpt-90) REVERT: D 86 ASP cc_start: 0.8810 (t70) cc_final: 0.8608 (t70) REVERT: D 231 ARG cc_start: 0.6994 (mtm180) cc_final: 0.6667 (mtt-85) REVERT: D 248 TYR cc_start: 0.9036 (t80) cc_final: 0.8831 (t80) REVERT: C 225 LEU cc_start: 0.8728 (mp) cc_final: 0.8512 (mp) outliers start: 14 outliers final: 4 residues processed: 146 average time/residue: 0.2439 time to fit residues: 52.3392 Evaluate side-chains 123 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain D residue 222 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 0.0980 chunk 95 optimal weight: 5.9990 chunk 38 optimal weight: 0.1980 chunk 141 optimal weight: 6.9990 chunk 152 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.8090 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 13065 Z= 0.173 Angle : 0.468 6.206 17780 Z= 0.238 Chirality : 0.045 0.137 1955 Planarity : 0.003 0.021 2265 Dihedral : 3.937 13.860 1715 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.95 % Allowed : 20.51 % Favored : 77.55 % 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: -0.03 (0.22), residues: 1540 helix: 0.73 (0.24), residues: 535 sheet: 1.47 (0.27), residues: 425 loop : -1.97 (0.24), residues: 580 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 0.006 0.001 PHE A 208 TYR 0.009 0.001 TYR D 38 ARG 0.003 0.000 ARG A 65 *********************** 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 158 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 131 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.8789 (t70) cc_final: 0.8587 (t70) REVERT: E 34 LYS cc_start: 0.9006 (mttp) cc_final: 0.8795 (mttm) REVERT: E 86 ASP cc_start: 0.8799 (t70) cc_final: 0.8349 (t70) REVERT: B 86 ASP cc_start: 0.8704 (t70) cc_final: 0.8342 (t70) REVERT: B 225 LEU cc_start: 0.8740 (mp) cc_final: 0.8458 (mp) outliers start: 27 outliers final: 21 residues processed: 155 average time/residue: 0.2335 time to fit residues: 53.5278 Evaluate side-chains 139 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 81 VAL 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 E residue 29 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 81 VAL 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 C residue 60 ASN Chi-restraints excluded: chain C residue 81 VAL 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: 5.9990 chunk 106 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN C 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13065 Z= 0.249 Angle : 0.496 5.792 17780 Z= 0.254 Chirality : 0.045 0.135 1955 Planarity : 0.003 0.020 2265 Dihedral : 4.094 16.831 1715 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.54 % Allowed : 19.35 % 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: 0.20 (0.22), residues: 1540 helix: 1.02 (0.24), residues: 535 sheet: 1.67 (0.27), residues: 420 loop : -1.97 (0.24), residues: 585 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 0.009 0.001 PHE D 208 TYR 0.012 0.001 TYR D 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 182 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 133 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.7847 (m110) REVERT: A 264 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8302 (mt0) REVERT: E 34 LYS cc_start: 0.9072 (mttp) cc_final: 0.8848 (mttm) REVERT: E 86 ASP cc_start: 0.8690 (t70) cc_final: 0.8308 (t70) REVERT: E 264 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8365 (mt0) REVERT: B 151 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.7856 (m110) REVERT: B 169 HIS cc_start: 0.7494 (t70) cc_final: 0.7229 (t70) REVERT: B 231 ARG cc_start: 0.7299 (mtm180) cc_final: 0.6852 (mtt-85) REVERT: D 30 GLU cc_start: 0.8851 (pm20) cc_final: 0.8495 (pm20) REVERT: D 136 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8420 (p0) REVERT: D 231 ARG cc_start: 0.7364 (mtm180) cc_final: 0.6572 (mtt-85) REVERT: D 264 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8204 (mt0) REVERT: C 136 ASN cc_start: 0.8920 (OUTLIER) cc_final: 0.8410 (p0) REVERT: C 151 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.8288 (t0) outliers start: 49 outliers final: 27 residues processed: 178 average time/residue: 0.2337 time to fit residues: 61.5990 Evaluate side-chains 162 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 127 time to evaluate : 1.496 ------------------------------------------------------------------------------- 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 151 ASN 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 60 ASN Chi-restraints excluded: chain E residue 214 LEU 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 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 B residue 222 VAL Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 136 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 81 VAL Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 214 LEU 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: 6.9990 chunk 111 optimal weight: 5.9990 chunk 61 optimal weight: 0.2980 chunk 127 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN E 298 GLN B 298 GLN D 298 GLN C 251 ASN C 298 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13065 Z= 0.402 Angle : 0.573 7.588 17780 Z= 0.295 Chirality : 0.047 0.136 1955 Planarity : 0.003 0.022 2265 Dihedral : 4.492 21.766 1715 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.97 % Allowed : 19.42 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.22), residues: 1540 helix: 0.89 (0.24), residues: 535 sheet: 1.44 (0.26), residues: 440 loop : -1.84 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 161 HIS 0.003 0.001 HIS A 177 PHE 0.010 0.001 PHE C 133 TYR 0.014 0.002 TYR E 204 ARG 0.002 0.000 ARG D 105 *********************** 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 182 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 127 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8060 (mmm-85) cc_final: 0.7727 (tpp80) REVERT: A 191 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.9083 (mt) REVERT: A 264 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8468 (mt0) REVERT: E 34 LYS cc_start: 0.9082 (mttp) cc_final: 0.8867 (mttm) REVERT: E 231 ARG cc_start: 0.7181 (mtm180) cc_final: 0.6929 (mtt180) REVERT: E 264 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8428 (mt0) REVERT: B 151 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.8088 (m110) REVERT: B 231 ARG cc_start: 0.7316 (mtm180) cc_final: 0.6782 (mtt-85) REVERT: D 30 GLU cc_start: 0.8932 (pm20) cc_final: 0.8593 (pm20) REVERT: D 136 ASN cc_start: 0.8940 (OUTLIER) cc_final: 0.8481 (p0) REVERT: D 151 ASN cc_start: 0.8332 (OUTLIER) cc_final: 0.8070 (m-40) REVERT: D 161 TRP cc_start: 0.8416 (m-10) cc_final: 0.8087 (m-10) REVERT: D 231 ARG cc_start: 0.7372 (mtm180) cc_final: 0.7094 (mtm180) REVERT: D 245 TYR cc_start: 0.7876 (m-10) cc_final: 0.7588 (m-80) REVERT: D 264 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8385 (mt0) REVERT: C 136 ASN cc_start: 0.9027 (OUTLIER) cc_final: 0.8473 (p0) REVERT: C 151 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8468 (t0) REVERT: C 184 ASN cc_start: 0.8409 (OUTLIER) cc_final: 0.8173 (m-40) outliers start: 55 outliers final: 31 residues processed: 176 average time/residue: 0.2424 time to fit residues: 62.2413 Evaluate side-chains 170 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 129 time to evaluate : 1.454 ------------------------------------------------------------------------------- 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 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 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 39 ILE 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 B residue 222 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 151 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 C residue 60 ASN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 136 ASN 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 253 LEU Chi-restraints excluded: chain C residue 265 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 69 optimal weight: 0.0770 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN B 264 GLN C 251 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13065 Z= 0.143 Angle : 0.469 8.208 17780 Z= 0.237 Chirality : 0.044 0.134 1955 Planarity : 0.002 0.024 2265 Dihedral : 4.046 14.596 1715 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.38 % Allowed : 20.94 % Favored : 76.68 % 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: 0.26 (0.22), residues: 1540 helix: 1.08 (0.24), residues: 535 sheet: 1.61 (0.27), residues: 415 loop : -1.85 (0.24), residues: 590 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 0.009 0.001 PHE B 208 TYR 0.008 0.001 TYR D 203 ARG 0.002 0.000 ARG D 141 *********************** 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 166 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 133 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8248 (mt-10) REVERT: A 264 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8234 (mt0) REVERT: E 230 GLU cc_start: 0.6860 (mp0) cc_final: 0.6636 (pm20) REVERT: B 30 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8383 (pm20) REVERT: B 231 ARG cc_start: 0.7284 (mtm180) cc_final: 0.6934 (mtt180) REVERT: D 30 GLU cc_start: 0.8832 (pm20) cc_final: 0.8510 (pm20) REVERT: D 65 ARG cc_start: 0.7688 (mmm-85) cc_final: 0.7317 (ttm-80) REVERT: D 161 TRP cc_start: 0.8264 (m-10) cc_final: 0.8016 (m-10) REVERT: C 30 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8451 (pm20) outliers start: 33 outliers final: 23 residues processed: 160 average time/residue: 0.2479 time to fit residues: 58.3852 Evaluate side-chains 155 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 128 time to evaluate : 1.603 ------------------------------------------------------------------------------- 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 222 VAL Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 306 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 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 157 ILE 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 265 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 84 optimal weight: 0.6980 chunk 126 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13065 Z= 0.292 Angle : 0.521 7.664 17780 Z= 0.266 Chirality : 0.046 0.133 1955 Planarity : 0.003 0.021 2265 Dihedral : 4.222 19.317 1715 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.39 % Allowed : 20.29 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.23), residues: 1540 helix: 1.09 (0.24), residues: 535 sheet: 1.46 (0.26), residues: 440 loop : -1.82 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 161 HIS 0.003 0.001 HIS A 285 PHE 0.011 0.001 PHE A 142 TYR 0.011 0.001 TYR E 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 175 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 128 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8331 (mt-10) REVERT: A 264 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8346 (mt0) REVERT: A 265 MET cc_start: 0.7757 (mtp) cc_final: 0.7392 (mtp) REVERT: A 304 PHE cc_start: 0.4932 (OUTLIER) cc_final: 0.4302 (t80) REVERT: E 231 ARG cc_start: 0.7510 (ttm170) cc_final: 0.7268 (ttm170) REVERT: B 30 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8154 (mp0) REVERT: B 231 ARG cc_start: 0.7316 (mtm180) cc_final: 0.7002 (mtt180) REVERT: D 30 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8532 (pm20) REVERT: D 65 ARG cc_start: 0.7736 (mmm-85) cc_final: 0.7355 (ttm-80) REVERT: D 136 ASN cc_start: 0.8881 (OUTLIER) cc_final: 0.8425 (p0) REVERT: D 161 TRP cc_start: 0.8375 (m-10) cc_final: 0.8049 (m-10) REVERT: D 245 TYR cc_start: 0.7699 (m-10) cc_final: 0.7428 (m-80) REVERT: D 264 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8274 (mt0) REVERT: C 30 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8402 (pm20) REVERT: C 136 ASN cc_start: 0.8977 (OUTLIER) cc_final: 0.8429 (p0) REVERT: C 304 PHE cc_start: 0.5290 (OUTLIER) cc_final: 0.4405 (t80) outliers start: 47 outliers final: 30 residues processed: 166 average time/residue: 0.2535 time to fit residues: 61.2799 Evaluate side-chains 167 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 127 time to evaluate : 1.457 ------------------------------------------------------------------------------- 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 184 ASN 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 A residue 304 PHE Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 306 LEU 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 185 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 VAL 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 136 ASN Chi-restraints excluded: chain D residue 157 ILE 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 30 GLU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 236 PHE 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: 20.0000 chunk 89 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13065 Z= 0.162 Angle : 0.472 7.043 17780 Z= 0.239 Chirality : 0.044 0.132 1955 Planarity : 0.002 0.024 2265 Dihedral : 4.002 15.656 1715 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.32 % Allowed : 20.07 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.23), residues: 1540 helix: 1.15 (0.24), residues: 535 sheet: 1.50 (0.26), residues: 435 loop : -1.81 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 206 HIS 0.003 0.001 HIS A 285 PHE 0.010 0.001 PHE E 228 TYR 0.009 0.001 TYR D 38 ARG 0.002 0.000 ARG D 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 189 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 143 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8274 (m-30) cc_final: 0.7801 (p0) REVERT: A 129 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8269 (mt-10) REVERT: A 264 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8252 (mt0) REVERT: A 265 MET cc_start: 0.7657 (mtp) cc_final: 0.7310 (mtp) REVERT: A 304 PHE cc_start: 0.4897 (OUTLIER) cc_final: 0.4273 (t80) REVERT: E 30 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8418 (pm20) REVERT: E 304 PHE cc_start: 0.4875 (OUTLIER) cc_final: 0.3602 (t80) REVERT: B 30 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8373 (pm20) REVERT: B 82 VAL cc_start: 0.9160 (t) cc_final: 0.8940 (t) REVERT: B 129 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7998 (mt-10) REVERT: B 231 ARG cc_start: 0.7259 (mtm180) cc_final: 0.6854 (mtt180) REVERT: B 304 PHE cc_start: 0.5077 (OUTLIER) cc_final: 0.4253 (t80) REVERT: D 30 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8501 (pm20) REVERT: D 65 ARG cc_start: 0.7748 (mmm-85) cc_final: 0.7328 (ttt180) REVERT: D 161 TRP cc_start: 0.8288 (m-10) cc_final: 0.8007 (m-10) REVERT: D 245 TYR cc_start: 0.7572 (m-10) cc_final: 0.7330 (m-80) REVERT: D 304 PHE cc_start: 0.4830 (OUTLIER) cc_final: 0.3887 (t80) REVERT: C 30 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8380 (pm20) REVERT: C 136 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8360 (p0) outliers start: 46 outliers final: 31 residues processed: 178 average time/residue: 0.2405 time to fit residues: 62.8409 Evaluate side-chains 176 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 133 time to evaluate : 1.472 ------------------------------------------------------------------------------- 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 184 ASN 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 235 SER 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 136 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 E residue 306 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 39 ILE Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 157 ILE 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 39 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 265 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 131 optimal weight: 0.0050 chunk 138 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 overall best weight: 1.7800 ------------------------------------------------------------------------------- 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 C 154 ASN C 251 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13065 Z= 0.254 Angle : 0.508 7.582 17780 Z= 0.259 Chirality : 0.045 0.132 1955 Planarity : 0.003 0.022 2265 Dihedral : 4.145 19.709 1715 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.90 % Allowed : 19.78 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.23), residues: 1540 helix: 1.12 (0.24), residues: 535 sheet: 1.46 (0.26), residues: 440 loop : -1.84 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 161 HIS 0.003 0.001 HIS D 285 PHE 0.015 0.001 PHE B 208 TYR 0.014 0.001 TYR B 248 ARG 0.003 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 184 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 130 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8348 (mt-10) REVERT: A 264 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8290 (mt0) REVERT: A 265 MET cc_start: 0.7842 (mtp) cc_final: 0.7492 (mtp) REVERT: A 304 PHE cc_start: 0.4965 (OUTLIER) cc_final: 0.4346 (t80) REVERT: E 30 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8419 (pm20) REVERT: E 304 PHE cc_start: 0.4926 (OUTLIER) cc_final: 0.3721 (t80) REVERT: B 30 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8080 (mp0) REVERT: B 82 VAL cc_start: 0.9173 (t) cc_final: 0.8947 (t) REVERT: B 129 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8108 (mt-10) REVERT: B 304 PHE cc_start: 0.5265 (OUTLIER) cc_final: 0.4354 (t80) REVERT: D 30 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8517 (pm20) REVERT: D 65 ARG cc_start: 0.7752 (mmm-85) cc_final: 0.7322 (ttt180) REVERT: D 136 ASN cc_start: 0.8837 (OUTLIER) cc_final: 0.8429 (p0) REVERT: D 151 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.8097 (m-40) REVERT: D 161 TRP cc_start: 0.8381 (m-10) cc_final: 0.8082 (m-10) REVERT: D 245 TYR cc_start: 0.7615 (m-10) cc_final: 0.7343 (m-80) REVERT: D 304 PHE cc_start: 0.4884 (OUTLIER) cc_final: 0.3929 (t80) REVERT: C 30 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8380 (pm20) REVERT: C 136 ASN cc_start: 0.8956 (OUTLIER) cc_final: 0.8405 (p0) REVERT: C 304 PHE cc_start: 0.5225 (OUTLIER) cc_final: 0.4315 (t80) outliers start: 54 outliers final: 32 residues processed: 171 average time/residue: 0.2596 time to fit residues: 64.9091 Evaluate side-chains 176 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 129 time to evaluate : 1.700 ------------------------------------------------------------------------------- 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 184 ASN 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 136 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 304 PHE Chi-restraints excluded: chain E residue 306 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 81 VAL Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 157 ILE 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 136 ASN Chi-restraints excluded: chain C residue 154 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: 5.9990 chunk 89 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 97 optimal weight: 0.0970 overall best weight: 2.3384 ------------------------------------------------------------------------------- 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 C 154 ASN C 251 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13065 Z= 0.316 Angle : 0.535 7.811 17780 Z= 0.274 Chirality : 0.046 0.130 1955 Planarity : 0.003 0.022 2265 Dihedral : 4.291 20.646 1715 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.97 % Allowed : 20.00 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.23), residues: 1540 helix: 1.06 (0.24), residues: 535 sheet: 1.42 (0.26), residues: 440 loop : -1.84 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 161 HIS 0.003 0.001 HIS A 285 PHE 0.015 0.001 PHE B 208 TYR 0.015 0.001 TYR B 248 ARG 0.002 0.000 ARG A 286 ********************** 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 189 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 134 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8305 (m-30) cc_final: 0.7838 (p0) REVERT: A 129 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8361 (mt-10) REVERT: A 264 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8369 (mt0) REVERT: A 265 MET cc_start: 0.7945 (mtp) cc_final: 0.7611 (mtp) REVERT: A 304 PHE cc_start: 0.4905 (OUTLIER) cc_final: 0.4309 (t80) REVERT: E 30 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8438 (pm20) REVERT: E 304 PHE cc_start: 0.4738 (OUTLIER) cc_final: 0.3723 (t80) REVERT: B 30 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8342 (pm20) REVERT: B 129 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8149 (mt-10) REVERT: B 304 PHE cc_start: 0.5080 (OUTLIER) cc_final: 0.4282 (t80) REVERT: D 30 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8544 (pm20) REVERT: D 65 ARG cc_start: 0.7778 (mmm-85) cc_final: 0.7329 (ttt180) REVERT: D 136 ASN cc_start: 0.8895 (OUTLIER) cc_final: 0.8462 (p0) REVERT: D 151 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.8064 (m-40) REVERT: D 161 TRP cc_start: 0.8408 (m-10) cc_final: 0.8024 (m-10) REVERT: D 231 ARG cc_start: 0.7360 (ttm170) cc_final: 0.6747 (mtt90) REVERT: D 245 TYR cc_start: 0.7681 (m-10) cc_final: 0.7418 (m-80) REVERT: D 304 PHE cc_start: 0.4935 (OUTLIER) cc_final: 0.3961 (t80) REVERT: C 30 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8409 (pm20) REVERT: C 136 ASN cc_start: 0.8987 (OUTLIER) cc_final: 0.8427 (p0) REVERT: C 304 PHE cc_start: 0.5335 (OUTLIER) cc_final: 0.4451 (t80) outliers start: 55 outliers final: 35 residues processed: 176 average time/residue: 0.2398 time to fit residues: 61.6736 Evaluate side-chains 182 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 132 time to evaluate : 1.578 ------------------------------------------------------------------------------- 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 184 ASN 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 136 ASN Chi-restraints excluded: chain E residue 154 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 E residue 306 LEU 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 154 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 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 81 VAL Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 154 ASN 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 136 ASN Chi-restraints excluded: chain C residue 154 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: 1.9990 chunk 37 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 C 251 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.129901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.096108 restraints weight = 15925.620| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.73 r_work: 0.2988 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13065 Z= 0.186 Angle : 0.486 7.767 17780 Z= 0.247 Chirality : 0.044 0.132 1955 Planarity : 0.002 0.023 2265 Dihedral : 4.078 20.100 1715 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.47 % Allowed : 20.43 % Favored : 76.10 % 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 (0.23), residues: 1540 helix: 1.13 (0.24), residues: 535 sheet: 1.44 (0.26), residues: 440 loop : -1.86 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 206 HIS 0.003 0.001 HIS A 285 PHE 0.009 0.001 PHE B 208 TYR 0.013 0.001 TYR B 248 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: 2499.39 seconds wall clock time: 45 minutes 16.09 seconds (2716.09 seconds total)