Starting phenix.real_space_refine on Sun Aug 24 01:31:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wbe_37422/08_2025/8wbe_37422_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wbe_37422/08_2025/8wbe_37422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wbe_37422/08_2025/8wbe_37422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wbe_37422/08_2025/8wbe_37422.map" model { file = "/net/cci-nas-00/data/ceres_data/8wbe_37422/08_2025/8wbe_37422_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wbe_37422/08_2025/8wbe_37422_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 sd= 0.148 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 126 5.16 5 C 10161 2.51 5 N 2769 2.21 5 O 3038 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16094 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2782 Classifications: {'peptide': 352} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 335} Chain: "B" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2596 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 314} Chain breaks: 1 Chain: "C" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2576 Classifications: {'peptide': 327} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 311} Chain breaks: 1 Chain: "a" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2782 Classifications: {'peptide': 352} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 335} Chain: "b" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2782 Classifications: {'peptide': 352} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 335} Chain: "c" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2576 Classifications: {'peptide': 327} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 311} Chain breaks: 1 Time building chain proxies: 3.74, per 1000 atoms: 0.23 Number of scatterers: 16094 At special positions: 0 Unit cell: (124.1, 125.8, 121.55, 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 126 16.00 O 3038 8.00 N 2769 7.00 C 10161 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 15 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 316 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 15 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 143 " distance=2.03 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 223 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 316 " distance=2.06 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 15 " distance=2.03 Simple disulfide: pdb=" SG CYS a 55 " - pdb=" SG CYS a 143 " distance=2.03 Simple disulfide: pdb=" SG CYS a 179 " - pdb=" SG CYS a 223 " distance=2.03 Simple disulfide: pdb=" SG CYS a 280 " - pdb=" SG CYS a 329 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " distance=2.03 Simple disulfide: pdb=" SG CYS b 4 " - pdb=" SG CYS b 15 " distance=2.03 Simple disulfide: pdb=" SG CYS b 55 " - pdb=" SG CYS b 143 " distance=2.03 Simple disulfide: pdb=" SG CYS b 179 " - pdb=" SG CYS b 223 " distance=2.03 Simple disulfide: pdb=" SG CYS b 280 " - pdb=" SG CYS b 329 " distance=2.03 Simple disulfide: pdb=" SG CYS b 313 " - pdb=" SG CYS b 316 " distance=2.03 Simple disulfide: pdb=" SG CYS c 4 " - pdb=" SG CYS c 15 " distance=2.03 Simple disulfide: pdb=" SG CYS c 55 " - pdb=" SG CYS c 143 " distance=2.03 Simple disulfide: pdb=" SG CYS c 179 " - pdb=" SG CYS c 223 " distance=2.03 Simple disulfide: pdb=" SG CYS c 280 " - pdb=" SG CYS c 329 " distance=2.03 Simple disulfide: pdb=" SG CYS c 313 " - pdb=" SG CYS c 316 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.90 Conformation dependent library (CDL) restraints added in 564.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3738 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 25 sheets defined 18.1% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 38 through 53 Processing helix chain 'A' and resid 61 through 82 removed outlier: 5.581A pdb=" N ASN A 73 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLU A 74 " --> pdb=" O GLN A 70 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 82 " --> pdb=" O VAL A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 180 through 183 removed outlier: 3.524A pdb=" N LEU A 183 " --> pdb=" O ASP A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 183' Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.528A pdb=" N THR A 230 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.718A pdb=" N ALA A 248 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 271 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'B' and resid 38 through 52 removed outlier: 3.685A pdb=" N LEU B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA B 43 " --> pdb=" O PRO B 39 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP B 52 " --> pdb=" O ASN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 72 removed outlier: 3.546A pdb=" N ILE B 66 " --> pdb=" O ARG B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 82 removed outlier: 3.594A pdb=" N TYR B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL B 78 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 180 through 183 removed outlier: 3.689A pdb=" N LEU B 183 " --> pdb=" O ASP B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 183' Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.634A pdb=" N THR B 230 " --> pdb=" O LYS B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 removed outlier: 3.600A pdb=" N ALA B 248 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 271 removed outlier: 3.541A pdb=" N LEU B 270 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 345 Processing helix chain 'C' and resid 40 through 53 removed outlier: 3.913A pdb=" N ILE C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 82 removed outlier: 5.170A pdb=" N ASN C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLU C 74 " --> pdb=" O GLN C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 148 Processing helix chain 'C' and resid 180 through 183 removed outlier: 3.747A pdb=" N LEU C 183 " --> pdb=" O ASP C 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 180 through 183' Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.612A pdb=" N THR C 230 " --> pdb=" O LYS C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 248 removed outlier: 3.678A pdb=" N ALA C 248 " --> pdb=" O LYS C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 271 removed outlier: 3.814A pdb=" N GLY C 271 " --> pdb=" O TRP C 268 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 53 Processing helix chain 'a' and resid 61 through 82 removed outlier: 3.642A pdb=" N ASN a 65 " --> pdb=" O THR a 61 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE a 66 " --> pdb=" O ARG a 62 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET a 67 " --> pdb=" O LEU a 63 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ASN a 73 " --> pdb=" O LYS a 69 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLU a 74 " --> pdb=" O GLN a 70 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 146 No H-bonds generated for 'chain 'a' and resid 144 through 146' Processing helix chain 'a' and resid 180 through 183 removed outlier: 3.709A pdb=" N LEU a 183 " --> pdb=" O ASP a 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 180 through 183' Processing helix chain 'a' and resid 226 through 230 removed outlier: 3.821A pdb=" N THR a 230 " --> pdb=" O LYS a 227 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 248 removed outlier: 3.590A pdb=" N ALA a 248 " --> pdb=" O LYS a 245 " (cutoff:3.500A) Processing helix chain 'a' and resid 267 through 271 removed outlier: 3.602A pdb=" N GLY a 271 " --> pdb=" O TRP a 268 " (cutoff:3.500A) Processing helix chain 'a' and resid 341 through 345 Processing helix chain 'b' and resid 38 through 51 Processing helix chain 'b' and resid 61 through 72 removed outlier: 3.578A pdb=" N ASN b 65 " --> pdb=" O THR b 61 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE b 66 " --> pdb=" O ARG b 62 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET b 67 " --> pdb=" O LEU b 63 " (cutoff:3.500A) Processing helix chain 'b' and resid 73 through 83 removed outlier: 3.853A pdb=" N GLY b 83 " --> pdb=" O LEU b 79 " (cutoff:3.500A) Processing helix chain 'b' and resid 144 through 148 removed outlier: 3.733A pdb=" N ARG b 148 " --> pdb=" O ASN b 145 " (cutoff:3.500A) Processing helix chain 'b' and resid 180 through 183 Processing helix chain 'b' and resid 226 through 230 Processing helix chain 'b' and resid 244 through 248 removed outlier: 3.516A pdb=" N ALA b 248 " --> pdb=" O LYS b 245 " (cutoff:3.500A) Processing helix chain 'c' and resid 38 through 53 removed outlier: 3.801A pdb=" N ALA c 43 " --> pdb=" O PRO c 39 " (cutoff:3.500A) Processing helix chain 'c' and resid 61 through 82 removed outlier: 3.671A pdb=" N ILE c 66 " --> pdb=" O ARG c 62 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N MET c 67 " --> pdb=" O LEU c 63 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ASN c 73 " --> pdb=" O LYS c 69 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N GLU c 74 " --> pdb=" O GLN c 70 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY c 82 " --> pdb=" O VAL c 78 " (cutoff:3.500A) Processing helix chain 'c' and resid 144 through 148 removed outlier: 3.562A pdb=" N ARG c 148 " --> pdb=" O ASN c 145 " (cutoff:3.500A) Processing helix chain 'c' and resid 180 through 183 removed outlier: 3.889A pdb=" N LEU c 183 " --> pdb=" O ASP c 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 180 through 183' Processing helix chain 'c' and resid 226 through 230 Processing helix chain 'c' and resid 244 through 248 removed outlier: 3.514A pdb=" N ALA c 248 " --> pdb=" O LYS c 245 " (cutoff:3.500A) Processing helix chain 'c' and resid 267 through 271 removed outlier: 3.725A pdb=" N LEU c 270 " --> pdb=" O PRO c 267 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY c 271 " --> pdb=" O TRP c 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 267 through 271' Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.227A pdb=" N LYS A 33 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N MET A 169 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLN A 35 " --> pdb=" O MET A 169 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N PHE A 171 " --> pdb=" O GLN A 35 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASN A 166 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N TYR A 158 " --> pdb=" O ASN A 166 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TRP A 168 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.821A pdb=" N THR A 87 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE A 135 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL A 89 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 331 removed outlier: 3.529A pdb=" N GLU A 274 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N PHE A 277 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N GLU A 213 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLU A 203 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA A 215 " --> pdb=" O TRP A 201 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP A 201 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP a 201 " --> pdb=" O ALA a 215 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA a 215 " --> pdb=" O TRP a 201 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLU a 203 " --> pdb=" O GLU a 213 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N GLU a 213 " --> pdb=" O PHE a 277 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE a 277 " --> pdb=" O GLU a 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 287 removed outlier: 5.952A pdb=" N THR A 284 " --> pdb=" O TRP A 311 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N CYS A 313 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N THR A 286 " --> pdb=" O CYS A 313 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 13 through 16 Processing sheet with id=AA7, first strand: chain 'B' and resid 34 through 35 removed outlier: 6.515A pdb=" N ASN B 166 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TYR B 158 " --> pdb=" O ASN B 166 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TRP B 168 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.903A pdb=" N GLY B 56 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 328 through 331 removed outlier: 3.881A pdb=" N GLY B 328 " --> pdb=" O GLY B 325 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B 274 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N PHE B 277 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N GLU B 213 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLU B 203 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA B 215 " --> pdb=" O TRP B 201 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TRP B 201 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N SER b 205 " --> pdb=" O ILE b 212 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE b 212 " --> pdb=" O SER b 205 " (cutoff:3.500A) removed outlier: 9.235A pdb=" N GLU b 213 " --> pdb=" O PHE b 277 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N PHE b 277 " --> pdb=" O GLU b 213 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU b 274 " --> pdb=" O LEU b 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 284 through 287 removed outlier: 6.250A pdb=" N THR B 284 " --> pdb=" O TRP B 311 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N CYS B 313 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR B 286 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 16 Processing sheet with id=AB3, first strand: chain 'C' and resid 32 through 35 removed outlier: 6.743A pdb=" N ASN C 166 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR C 158 " --> pdb=" O ASN C 166 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TRP C 168 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 89 through 90 removed outlier: 6.221A pdb=" N VAL C 89 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE C 57 " --> pdb=" O LEU C 134 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 210 through 214 removed outlier: 6.942A pdb=" N GLU C 203 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 196 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TRP c 201 " --> pdb=" O ALA c 215 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA c 215 " --> pdb=" O TRP c 201 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLU c 203 " --> pdb=" O GLU c 213 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N GLU c 213 " --> pdb=" O PHE c 277 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE c 277 " --> pdb=" O GLU c 213 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 274 through 277 Processing sheet with id=AB7, first strand: chain 'C' and resid 285 through 287 removed outlier: 6.155A pdb=" N THR C 286 " --> pdb=" O CYS C 313 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'a' and resid 33 through 35 removed outlier: 6.542A pdb=" N ASN a 166 " --> pdb=" O TYR a 158 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N TYR a 158 " --> pdb=" O ASN a 166 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TRP a 168 " --> pdb=" O GLU a 156 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'a' and resid 87 through 90 removed outlier: 6.871A pdb=" N THR a 87 " --> pdb=" O PHE a 133 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE a 135 " --> pdb=" O THR a 87 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL a 89 " --> pdb=" O ILE a 135 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY a 56 " --> pdb=" O ALA a 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'a' and resid 284 through 287 removed outlier: 6.163A pdb=" N THR a 284 " --> pdb=" O TRP a 311 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N CYS a 313 " --> pdb=" O THR a 284 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR a 286 " --> pdb=" O CYS a 313 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'b' and resid 32 through 35 removed outlier: 6.323A pdb=" N LYS b 33 " --> pdb=" O ILE b 167 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N MET b 169 " --> pdb=" O LYS b 33 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN b 35 " --> pdb=" O MET b 169 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N PHE b 171 " --> pdb=" O GLN b 35 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN b 166 " --> pdb=" O TYR b 158 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TYR b 158 " --> pdb=" O ASN b 166 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TRP b 168 " --> pdb=" O GLU b 156 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'b' and resid 87 through 90 removed outlier: 7.243A pdb=" N THR b 87 " --> pdb=" O PHE b 133 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE b 135 " --> pdb=" O THR b 87 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL b 89 " --> pdb=" O ILE b 135 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'b' and resid 284 through 287 removed outlier: 6.521A pdb=" N THR b 284 " --> pdb=" O TRP b 311 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N CYS b 313 " --> pdb=" O THR b 284 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR b 286 " --> pdb=" O CYS b 313 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'c' and resid 33 through 35 removed outlier: 7.023A pdb=" N TRP c 168 " --> pdb=" O GLU c 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'c' and resid 89 through 90 removed outlier: 6.478A pdb=" N VAL c 89 " --> pdb=" O ILE c 135 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'c' and resid 284 through 287 423 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.53 Time building geometry restraints manager: 1.25 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: 5216 1.34 - 1.46: 3962 1.46 - 1.58: 7156 1.58 - 1.71: 0 1.71 - 1.83: 180 Bond restraints: 16514 Sorted by residual: bond pdb=" N TRP B 80 " pdb=" CA TRP B 80 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.32e-02 5.74e+03 7.15e+00 bond pdb=" N ASN B 76 " pdb=" CA ASN B 76 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.25e-02 6.40e+03 6.42e+00 bond pdb=" N LEU B 75 " pdb=" CA LEU B 75 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.32e-02 5.74e+03 6.31e+00 bond pdb=" N VAL B 78 " pdb=" CA VAL B 78 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.17e-02 7.31e+03 6.23e+00 bond pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.30e-02 5.92e+03 5.80e+00 ... (remaining 16509 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 21575 1.23 - 2.47: 658 2.47 - 3.70: 147 3.70 - 4.94: 13 4.94 - 6.17: 9 Bond angle restraints: 22402 Sorted by residual: angle pdb=" N LEU B 75 " pdb=" CA LEU B 75 " pdb=" C LEU B 75 " ideal model delta sigma weight residual 113.20 108.63 4.57 1.21e+00 6.83e-01 1.43e+01 angle pdb=" N THR C 317 " pdb=" CA THR C 317 " pdb=" C THR C 317 " ideal model delta sigma weight residual 109.40 103.40 6.00 1.63e+00 3.76e-01 1.35e+01 angle pdb=" CA THR C 317 " pdb=" C THR C 317 " pdb=" O THR C 317 " ideal model delta sigma weight residual 120.70 117.12 3.58 1.08e+00 8.57e-01 1.10e+01 angle pdb=" CA GLU B 81 " pdb=" C GLU B 81 " pdb=" O GLU B 81 " ideal model delta sigma weight residual 120.51 115.87 4.64 1.43e+00 4.89e-01 1.05e+01 angle pdb=" C THR a 27 " pdb=" N TRP a 28 " pdb=" CA TRP a 28 " ideal model delta sigma weight residual 121.54 127.63 -6.09 1.91e+00 2.74e-01 1.02e+01 ... (remaining 22397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 8851 17.38 - 34.75: 783 34.75 - 52.13: 132 52.13 - 69.50: 28 69.50 - 86.88: 13 Dihedral angle restraints: 9807 sinusoidal: 3987 harmonic: 5820 Sorted by residual: dihedral pdb=" CB CYS A 313 " pdb=" SG CYS A 313 " pdb=" SG CYS A 316 " pdb=" CB CYS A 316 " ideal model delta sinusoidal sigma weight residual 93.00 173.67 -80.67 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CB CYS a 55 " pdb=" SG CYS a 55 " pdb=" SG CYS a 143 " pdb=" CB CYS a 143 " ideal model delta sinusoidal sigma weight residual -86.00 -141.86 55.86 1 1.00e+01 1.00e-02 4.21e+01 dihedral pdb=" CA TYR B 158 " pdb=" C TYR B 158 " pdb=" N GLY B 159 " pdb=" CA GLY B 159 " ideal model delta harmonic sigma weight residual 180.00 152.36 27.64 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 9804 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1613 0.037 - 0.074: 554 0.074 - 0.111: 171 0.111 - 0.148: 45 0.148 - 0.184: 4 Chirality restraints: 2387 Sorted by residual: chirality pdb=" CA THR C 317 " pdb=" N THR C 317 " pdb=" C THR C 317 " pdb=" CB THR C 317 " both_signs ideal model delta sigma weight residual False 2.53 2.71 -0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CA LEU C 321 " pdb=" N LEU C 321 " pdb=" C LEU C 321 " pdb=" CB LEU C 321 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.32e-01 chirality pdb=" CB ILE C 287 " pdb=" CA ILE C 287 " pdb=" CG1 ILE C 287 " pdb=" CG2 ILE C 287 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 2384 not shown) Planarity restraints: 2862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 75 " 0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C LEU B 75 " -0.073 2.00e-02 2.50e+03 pdb=" O LEU B 75 " 0.027 2.00e-02 2.50e+03 pdb=" N ASN B 76 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 74 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.76e+00 pdb=" C GLU B 74 " 0.045 2.00e-02 2.50e+03 pdb=" O GLU B 74 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU B 75 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 81 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" C GLU B 81 " -0.040 2.00e-02 2.50e+03 pdb=" O GLU B 81 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY B 82 " 0.014 2.00e-02 2.50e+03 ... (remaining 2859 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1094 2.74 - 3.28: 14705 3.28 - 3.82: 24684 3.82 - 4.36: 31902 4.36 - 4.90: 55270 Nonbonded interactions: 127655 Sorted by model distance: nonbonded pdb=" OD2 ASP A 197 " pdb=" NZ LYS A 221 " model vdw 2.196 3.120 nonbonded pdb=" O THR B 262 " pdb=" NH2 ARG B 294 " model vdw 2.198 3.120 nonbonded pdb=" O ASP b 23 " pdb=" OG1 THR b 27 " model vdw 2.203 3.040 nonbonded pdb=" O THR c 262 " pdb=" NH2 ARG c 294 " model vdw 2.217 3.120 nonbonded pdb=" OD2 ASP a 197 " pdb=" NZ LYS a 221 " model vdw 2.226 3.120 ... (remaining 127650 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 107 or resid 133 through 352)) selection = (chain 'B' and (resid 1 through 107 or resid 133 through 352)) selection = chain 'C' selection = (chain 'a' and (resid 1 through 107 or resid 133 through 352)) selection = (chain 'b' and (resid 1 through 107 or resid 133 through 352)) selection = chain 'c' } 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: 1.790 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: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.810 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 : 0.002 0.038 16544 Z= 0.128 Angle : 0.543 6.172 22462 Z= 0.310 Chirality : 0.042 0.184 2387 Planarity : 0.003 0.053 2862 Dihedral : 13.421 86.876 5979 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.04 % Favored : 94.91 % Rotamer: Outliers : 0.23 % Allowed : 0.23 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.18), residues: 2022 helix: 0.97 (0.37), residues: 224 sheet: -2.23 (0.22), residues: 513 loop : -1.10 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 148 TYR 0.017 0.001 TYR B 158 PHE 0.024 0.001 PHE b 20 TRP 0.018 0.001 TRP B 80 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00231 (16514) covalent geometry : angle 0.53953 (22402) SS BOND : bond 0.00513 ( 30) SS BOND : angle 1.33211 ( 60) hydrogen bonds : bond 0.25579 ( 423) hydrogen bonds : angle 9.07223 ( 1086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 343 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7032 (m-90) cc_final: 0.6587 (p-90) REVERT: A 70 GLN cc_start: 0.7309 (tt0) cc_final: 0.6819 (tt0) REVERT: A 272 LYS cc_start: 0.8809 (mttp) cc_final: 0.8367 (mtpm) REVERT: A 309 THR cc_start: 0.8395 (m) cc_final: 0.8146 (p) REVERT: B 17 SER cc_start: 0.9000 (p) cc_final: 0.8765 (t) REVERT: B 30 GLU cc_start: 0.8491 (pt0) cc_final: 0.7735 (mm-30) REVERT: B 35 GLN cc_start: 0.7239 (mm-40) cc_final: 0.7011 (mm110) REVERT: B 59 SER cc_start: 0.8840 (m) cc_final: 0.8434 (p) REVERT: B 70 GLN cc_start: 0.6983 (mt0) cc_final: 0.6736 (mp10) REVERT: B 166 ASN cc_start: 0.8086 (m-40) cc_final: 0.7784 (m-40) REVERT: B 168 TRP cc_start: 0.7647 (m100) cc_final: 0.7236 (m100) REVERT: B 214 LYS cc_start: 0.8234 (mtmt) cc_final: 0.7971 (mtpp) REVERT: B 274 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7631 (tp30) REVERT: B 340 GLU cc_start: 0.5594 (tm-30) cc_final: 0.5182 (tm-30) REVERT: C 12 GLU cc_start: 0.7039 (tt0) cc_final: 0.6637 (tt0) REVERT: C 14 LYS cc_start: 0.8682 (tptm) cc_final: 0.8342 (tptp) REVERT: C 23 ASP cc_start: 0.8182 (t0) cc_final: 0.7809 (t70) REVERT: C 35 GLN cc_start: 0.7382 (tp40) cc_final: 0.7138 (tp40) REVERT: C 74 GLU cc_start: 0.6436 (mt-10) cc_final: 0.6067 (mp0) REVERT: C 177 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6957 (tt0) REVERT: C 274 GLU cc_start: 0.7513 (tp30) cc_final: 0.7217 (tp30) REVERT: a 55 CYS cc_start: 0.6994 (t) cc_final: 0.6739 (p) REVERT: a 74 GLU cc_start: 0.6553 (mt-10) cc_final: 0.6192 (mp0) REVERT: a 214 LYS cc_start: 0.8342 (mtmt) cc_final: 0.7862 (mtpp) REVERT: a 240 GLN cc_start: 0.8768 (mm110) cc_final: 0.8370 (mm110) REVERT: a 314 ARG cc_start: 0.6720 (ttm170) cc_final: 0.6409 (ttm170) REVERT: a 344 ASN cc_start: 0.7197 (t0) cc_final: 0.6960 (m110) REVERT: b 14 LYS cc_start: 0.8325 (tptt) cc_final: 0.8074 (tptp) REVERT: b 92 ASP cc_start: 0.6581 (p0) cc_final: 0.6126 (p0) REVERT: b 99 LYS cc_start: 0.8149 (ttpp) cc_final: 0.7704 (tttp) REVERT: b 324 LEU cc_start: 0.8554 (mp) cc_final: 0.8343 (mt) REVERT: c 99 LYS cc_start: 0.7025 (ttmt) cc_final: 0.6630 (ttpp) REVERT: c 168 TRP cc_start: 0.6784 (m100) cc_final: 0.6472 (m100) outliers start: 4 outliers final: 3 residues processed: 347 average time/residue: 0.5825 time to fit residues: 223.0246 Evaluate side-chains 244 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 241 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain c residue 65 ASN Chi-restraints excluded: chain c residue 218 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 48 ASN a 65 ASN b 48 ASN b 76 ASN b 84 HIS c 166 ASN c 181 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.202522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.133114 restraints weight = 16327.761| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.92 r_work: 0.3202 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 16544 Z= 0.205 Angle : 0.589 7.767 22462 Z= 0.311 Chirality : 0.044 0.138 2387 Planarity : 0.004 0.040 2862 Dihedral : 4.995 44.359 2172 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.63 % Allowed : 10.01 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.18), residues: 2022 helix: 1.34 (0.37), residues: 225 sheet: -1.81 (0.22), residues: 539 loop : -1.15 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 148 TYR 0.016 0.002 TYR c 256 PHE 0.029 0.002 PHE b 20 TRP 0.015 0.002 TRP b 330 HIS 0.006 0.001 HIS a 50 Details of bonding type rmsd covalent geometry : bond 0.00498 (16514) covalent geometry : angle 0.58500 (22402) SS BOND : bond 0.00275 ( 30) SS BOND : angle 1.38934 ( 60) hydrogen bonds : bond 0.05275 ( 423) hydrogen bonds : angle 6.06321 ( 1086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 255 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7183 (m-90) cc_final: 0.6890 (p-90) REVERT: A 70 GLN cc_start: 0.7605 (tt0) cc_final: 0.7090 (tt0) REVERT: A 102 ARG cc_start: 0.7892 (mmm-85) cc_final: 0.7407 (mmt90) REVERT: A 272 LYS cc_start: 0.8807 (mttp) cc_final: 0.8392 (mtpm) REVERT: A 309 THR cc_start: 0.8597 (m) cc_final: 0.8292 (p) REVERT: A 314 ARG cc_start: 0.7103 (ttp-170) cc_final: 0.6895 (ttm-80) REVERT: B 31 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7243 (mm-40) REVERT: B 59 SER cc_start: 0.8849 (m) cc_final: 0.8611 (p) REVERT: B 70 GLN cc_start: 0.7260 (mt0) cc_final: 0.6953 (mp10) REVERT: B 76 ASN cc_start: 0.6205 (m-40) cc_final: 0.5733 (m110) REVERT: B 89 VAL cc_start: 0.7116 (t) cc_final: 0.6581 (m) REVERT: B 142 GLU cc_start: 0.6299 (pt0) cc_final: 0.5818 (tm-30) REVERT: B 154 GLU cc_start: 0.7894 (pt0) cc_final: 0.7353 (pt0) REVERT: B 168 TRP cc_start: 0.7941 (m100) cc_final: 0.7574 (m100) REVERT: B 274 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7770 (tp30) REVERT: C 12 GLU cc_start: 0.7214 (tt0) cc_final: 0.6863 (tt0) REVERT: C 14 LYS cc_start: 0.8283 (tptm) cc_final: 0.8040 (tptp) REVERT: C 74 GLU cc_start: 0.6665 (mt-10) cc_final: 0.6197 (mp0) REVERT: C 101 LYS cc_start: 0.7234 (mptt) cc_final: 0.6934 (mppt) REVERT: C 177 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7038 (tt0) REVERT: C 214 LYS cc_start: 0.7606 (ptmm) cc_final: 0.7250 (pptt) REVERT: C 274 GLU cc_start: 0.7377 (tp30) cc_final: 0.7170 (tp30) REVERT: a 30 GLU cc_start: 0.8135 (tt0) cc_final: 0.7630 (tt0) REVERT: a 74 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6615 (mp0) REVERT: a 214 LYS cc_start: 0.8612 (mtmt) cc_final: 0.8322 (mtpp) REVERT: a 240 GLN cc_start: 0.8809 (mm110) cc_final: 0.8414 (mm110) REVERT: a 287 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.8049 (mm) REVERT: a 314 ARG cc_start: 0.7037 (ttm170) cc_final: 0.6762 (ttm170) REVERT: b 48 ASN cc_start: 0.7707 (m-40) cc_final: 0.7495 (m110) REVERT: b 147 ARG cc_start: 0.6823 (ptm160) cc_final: 0.6476 (ptm160) REVERT: b 157 ASP cc_start: 0.8126 (p0) cc_final: 0.7764 (t0) REVERT: c 41 ARG cc_start: 0.7382 (ttt90) cc_final: 0.7163 (tpt90) REVERT: c 99 LYS cc_start: 0.7161 (ttmt) cc_final: 0.6888 (ttpp) REVERT: c 146 GLU cc_start: 0.5708 (pt0) cc_final: 0.5445 (mp0) REVERT: c 154 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7026 (mt-10) REVERT: c 168 TRP cc_start: 0.7200 (m100) cc_final: 0.6899 (m100) REVERT: c 197 ASP cc_start: 0.8349 (p0) cc_final: 0.8026 (p0) REVERT: c 318 MET cc_start: 0.7760 (mpp) cc_final: 0.7518 (mpm) REVERT: c 340 GLU cc_start: 0.4992 (tp30) cc_final: 0.4646 (tp30) outliers start: 46 outliers final: 21 residues processed: 281 average time/residue: 0.5827 time to fit residues: 180.4273 Evaluate side-chains 260 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 236 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 177 GLU Chi-restraints excluded: chain b residue 348 SER Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 324 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 37 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 158 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN C 145 ASN a 48 ASN b 293 HIS c 166 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.201774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.132264 restraints weight = 16541.256| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.96 r_work: 0.3314 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16544 Z= 0.212 Angle : 0.582 6.147 22462 Z= 0.307 Chirality : 0.045 0.147 2387 Planarity : 0.004 0.031 2862 Dihedral : 4.949 35.593 2168 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.43 % Allowed : 13.44 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.19), residues: 2022 helix: 1.42 (0.37), residues: 222 sheet: -1.89 (0.23), residues: 497 loop : -1.09 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 148 TYR 0.017 0.002 TYR c 256 PHE 0.022 0.002 PHE b 20 TRP 0.014 0.002 TRP b 330 HIS 0.006 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00520 (16514) covalent geometry : angle 0.57977 (22402) SS BOND : bond 0.00202 ( 30) SS BOND : angle 1.21019 ( 60) hydrogen bonds : bond 0.04724 ( 423) hydrogen bonds : angle 5.70621 ( 1086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 246 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7107 (m-90) cc_final: 0.6605 (p-90) REVERT: A 70 GLN cc_start: 0.7346 (tt0) cc_final: 0.6857 (tt0) REVERT: A 102 ARG cc_start: 0.7709 (mmm-85) cc_final: 0.7266 (mmt90) REVERT: A 309 THR cc_start: 0.8465 (m) cc_final: 0.8094 (p) REVERT: A 314 ARG cc_start: 0.7151 (ttp-170) cc_final: 0.6929 (ttm-80) REVERT: B 31 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7317 (mm-40) REVERT: B 59 SER cc_start: 0.8872 (m) cc_final: 0.8642 (p) REVERT: B 70 GLN cc_start: 0.7163 (mt0) cc_final: 0.6768 (mp10) REVERT: B 76 ASN cc_start: 0.6148 (m-40) cc_final: 0.5788 (m110) REVERT: B 89 VAL cc_start: 0.7000 (t) cc_final: 0.6426 (m) REVERT: B 142 GLU cc_start: 0.6488 (pt0) cc_final: 0.5905 (tm-30) REVERT: B 154 GLU cc_start: 0.7876 (pt0) cc_final: 0.7484 (pt0) REVERT: B 168 TRP cc_start: 0.7788 (m100) cc_final: 0.7506 (m100) REVERT: B 274 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7641 (tp30) REVERT: C 14 LYS cc_start: 0.8176 (tptm) cc_final: 0.7895 (tptp) REVERT: C 62 ARG cc_start: 0.7171 (ppt170) cc_final: 0.6877 (ttp80) REVERT: C 74 GLU cc_start: 0.6535 (mt-10) cc_final: 0.6085 (mp0) REVERT: C 101 LYS cc_start: 0.7101 (mptt) cc_final: 0.6800 (mppt) REVERT: C 177 GLU cc_start: 0.7445 (mt-10) cc_final: 0.6750 (tt0) REVERT: C 214 LYS cc_start: 0.7545 (ptmm) cc_final: 0.7126 (pptt) REVERT: C 258 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.6506 (tm-30) REVERT: C 274 GLU cc_start: 0.7430 (tp30) cc_final: 0.7197 (tp30) REVERT: a 30 GLU cc_start: 0.8282 (tt0) cc_final: 0.7682 (tt0) REVERT: a 74 GLU cc_start: 0.6859 (mt-10) cc_final: 0.6443 (mp0) REVERT: a 214 LYS cc_start: 0.8684 (mtmt) cc_final: 0.8323 (mtpp) REVERT: a 287 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.7987 (mm) REVERT: a 314 ARG cc_start: 0.6914 (ttm170) cc_final: 0.6620 (ttm170) REVERT: b 48 ASN cc_start: 0.7555 (m-40) cc_final: 0.7311 (m110) REVERT: b 147 ARG cc_start: 0.6549 (ptm160) cc_final: 0.6207 (ptt90) REVERT: b 157 ASP cc_start: 0.8154 (p0) cc_final: 0.7618 (t0) REVERT: b 180 ASP cc_start: 0.8424 (t0) cc_final: 0.8179 (t0) REVERT: c 148 ARG cc_start: 0.4854 (OUTLIER) cc_final: 0.3533 (tpp80) REVERT: c 154 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6878 (mt-10) REVERT: c 168 TRP cc_start: 0.6971 (m100) cc_final: 0.6764 (m100) REVERT: c 197 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8140 (p0) REVERT: c 276 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7261 (m-30) REVERT: c 318 MET cc_start: 0.7700 (mpp) cc_final: 0.7451 (mpm) REVERT: c 340 GLU cc_start: 0.4784 (tp30) cc_final: 0.4424 (tp30) outliers start: 60 outliers final: 29 residues processed: 274 average time/residue: 0.5835 time to fit residues: 175.9319 Evaluate side-chains 263 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 227 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 177 GLU Chi-restraints excluded: chain b residue 293 HIS Chi-restraints excluded: chain b residue 307 LEU Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain b residue 348 SER Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 65 ASN Chi-restraints excluded: chain c residue 148 ARG Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 197 ASP Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 212 ILE Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 276 ASP Chi-restraints excluded: chain c residue 324 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 152 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 97 optimal weight: 0.0770 chunk 23 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN B 207 ASN a 48 ASN c 166 ASN c 349 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.203498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.131308 restraints weight = 16304.589| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.01 r_work: 0.3268 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16544 Z= 0.128 Angle : 0.518 7.395 22462 Z= 0.274 Chirality : 0.042 0.132 2387 Planarity : 0.003 0.031 2862 Dihedral : 4.684 35.312 2168 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.54 % Allowed : 14.87 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.19), residues: 2022 helix: 1.48 (0.36), residues: 225 sheet: -1.77 (0.23), residues: 503 loop : -0.98 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 336 TYR 0.017 0.001 TYR c 256 PHE 0.014 0.001 PHE b 20 TRP 0.012 0.001 TRP B 80 HIS 0.006 0.001 HIS b 293 Details of bonding type rmsd covalent geometry : bond 0.00305 (16514) covalent geometry : angle 0.51582 (22402) SS BOND : bond 0.00189 ( 30) SS BOND : angle 1.03416 ( 60) hydrogen bonds : bond 0.03600 ( 423) hydrogen bonds : angle 5.40167 ( 1086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 239 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7172 (m-90) cc_final: 0.6868 (p-90) REVERT: A 70 GLN cc_start: 0.7528 (tt0) cc_final: 0.7107 (tt0) REVERT: A 102 ARG cc_start: 0.7852 (mmm-85) cc_final: 0.7437 (mmt90) REVERT: A 272 LYS cc_start: 0.8805 (mttp) cc_final: 0.8379 (mtpm) REVERT: A 314 ARG cc_start: 0.7315 (ttp-170) cc_final: 0.7043 (ttm-80) REVERT: B 31 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7373 (mm-40) REVERT: B 70 GLN cc_start: 0.7300 (mt0) cc_final: 0.6982 (mp10) REVERT: B 76 ASN cc_start: 0.6296 (m-40) cc_final: 0.5956 (m110) REVERT: B 89 VAL cc_start: 0.7283 (t) cc_final: 0.6744 (m) REVERT: B 142 GLU cc_start: 0.6550 (pt0) cc_final: 0.5994 (tm-30) REVERT: B 147 ARG cc_start: 0.8069 (mtp85) cc_final: 0.7790 (mtp85) REVERT: B 154 GLU cc_start: 0.7920 (pt0) cc_final: 0.7651 (pt0) REVERT: B 168 TRP cc_start: 0.7905 (m100) cc_final: 0.7605 (m100) REVERT: B 213 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7928 (pt0) REVERT: B 238 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7755 (mm-30) REVERT: B 274 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7679 (tp30) REVERT: C 14 LYS cc_start: 0.8184 (tptm) cc_final: 0.7887 (tptp) REVERT: C 62 ARG cc_start: 0.7197 (ppt170) cc_final: 0.6785 (ttp-110) REVERT: C 74 GLU cc_start: 0.6583 (mt-10) cc_final: 0.6024 (mp0) REVERT: C 101 LYS cc_start: 0.7260 (mptt) cc_final: 0.6636 (mppt) REVERT: C 177 GLU cc_start: 0.7511 (mt-10) cc_final: 0.6891 (tt0) REVERT: C 214 LYS cc_start: 0.7624 (ptmm) cc_final: 0.7281 (pptt) REVERT: a 30 GLU cc_start: 0.8142 (tt0) cc_final: 0.7620 (tt0) REVERT: a 74 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6470 (mp0) REVERT: a 101 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.7850 (mttt) REVERT: a 214 LYS cc_start: 0.8560 (mtmt) cc_final: 0.8266 (mtpp) REVERT: a 287 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8061 (mm) REVERT: a 314 ARG cc_start: 0.7102 (ttm170) cc_final: 0.6668 (ttm170) REVERT: b 48 ASN cc_start: 0.7705 (m-40) cc_final: 0.7457 (m110) REVERT: b 147 ARG cc_start: 0.6855 (ptm160) cc_final: 0.6626 (mtm110) REVERT: b 157 ASP cc_start: 0.8117 (p0) cc_final: 0.7774 (t0) REVERT: c 154 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7133 (mt-10) REVERT: c 168 TRP cc_start: 0.7217 (m100) cc_final: 0.7011 (m100) REVERT: c 197 ASP cc_start: 0.8240 (p0) cc_final: 0.7899 (p0) REVERT: c 276 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7333 (m-30) REVERT: c 318 MET cc_start: 0.7658 (mpp) cc_final: 0.7398 (mpm) REVERT: c 340 GLU cc_start: 0.4902 (tp30) cc_final: 0.4666 (tp30) REVERT: c 349 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.7055 (mp10) outliers start: 62 outliers final: 31 residues processed: 276 average time/residue: 0.5684 time to fit residues: 173.8697 Evaluate side-chains 260 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 101 LYS Chi-restraints excluded: chain a residue 208 GLN Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain a residue 344 ASN Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 177 GLU Chi-restraints excluded: chain b residue 307 LEU Chi-restraints excluded: chain b residue 348 SER Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 65 ASN Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 276 ASP Chi-restraints excluded: chain c residue 324 LEU Chi-restraints excluded: chain c residue 349 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 180 optimal weight: 20.0000 chunk 122 optimal weight: 0.0980 chunk 176 optimal weight: 9.9990 chunk 177 optimal weight: 8.9990 chunk 181 optimal weight: 6.9990 chunk 197 optimal weight: 20.0000 chunk 188 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN B 207 ASN C 254 HIS a 48 ASN c 166 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.198908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.132894 restraints weight = 16455.606| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.65 r_work: 0.3297 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 16544 Z= 0.288 Angle : 0.648 7.799 22462 Z= 0.340 Chirality : 0.047 0.184 2387 Planarity : 0.004 0.041 2862 Dihedral : 5.185 40.203 2168 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.32 % Favored : 92.63 % Rotamer: Outliers : 4.00 % Allowed : 16.07 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.18), residues: 2022 helix: 1.37 (0.36), residues: 223 sheet: -2.07 (0.22), residues: 521 loop : -1.14 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 294 TYR 0.020 0.002 TYR A 256 PHE 0.018 0.002 PHE b 20 TRP 0.018 0.002 TRP C 330 HIS 0.006 0.002 HIS c 269 Details of bonding type rmsd covalent geometry : bond 0.00708 (16514) covalent geometry : angle 0.64298 (22402) SS BOND : bond 0.00286 ( 30) SS BOND : angle 1.62380 ( 60) hydrogen bonds : bond 0.05069 ( 423) hydrogen bonds : angle 5.63337 ( 1086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 228 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7126 (m-90) cc_final: 0.6644 (p-90) REVERT: A 70 GLN cc_start: 0.7348 (tt0) cc_final: 0.6815 (tt0) REVERT: A 102 ARG cc_start: 0.7760 (mmm-85) cc_final: 0.7273 (mmt90) REVERT: A 272 LYS cc_start: 0.8819 (mttp) cc_final: 0.8271 (mtpm) REVERT: A 314 ARG cc_start: 0.7247 (ttp-170) cc_final: 0.6866 (ttm-80) REVERT: B 31 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7376 (mm-40) REVERT: B 70 GLN cc_start: 0.7277 (mt0) cc_final: 0.6849 (mp10) REVERT: B 142 GLU cc_start: 0.6613 (pt0) cc_final: 0.5952 (tm-30) REVERT: B 147 ARG cc_start: 0.7880 (mtp85) cc_final: 0.7540 (mtp85) REVERT: B 168 TRP cc_start: 0.7723 (m100) cc_final: 0.7512 (m100) REVERT: B 213 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7958 (pt0) REVERT: B 274 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7616 (tp30) REVERT: C 14 LYS cc_start: 0.8205 (tptm) cc_final: 0.7913 (tptp) REVERT: C 62 ARG cc_start: 0.7285 (ppt170) cc_final: 0.6919 (ttp80) REVERT: C 74 GLU cc_start: 0.6564 (mt-10) cc_final: 0.6070 (mp0) REVERT: C 101 LYS cc_start: 0.7209 (mptt) cc_final: 0.6885 (mppt) REVERT: C 177 GLU cc_start: 0.7469 (mt-10) cc_final: 0.6621 (tt0) REVERT: C 214 LYS cc_start: 0.7525 (ptmm) cc_final: 0.7132 (pptt) REVERT: a 74 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6495 (mp0) REVERT: a 101 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.7769 (mttt) REVERT: a 314 ARG cc_start: 0.6826 (ttm170) cc_final: 0.6337 (ttm170) REVERT: b 147 ARG cc_start: 0.6596 (ptm160) cc_final: 0.6017 (mtm-85) REVERT: b 157 ASP cc_start: 0.8180 (p0) cc_final: 0.7638 (t0) REVERT: c 154 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7010 (mt-10) REVERT: c 228 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.8106 (p) REVERT: c 276 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7275 (m-30) REVERT: c 318 MET cc_start: 0.7670 (mpp) cc_final: 0.7413 (mpm) REVERT: c 340 GLU cc_start: 0.4917 (tp30) cc_final: 0.4587 (tp30) REVERT: c 349 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.6879 (mp10) outliers start: 70 outliers final: 41 residues processed: 266 average time/residue: 0.5668 time to fit residues: 166.4256 Evaluate side-chains 268 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 220 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 101 LYS Chi-restraints excluded: chain a residue 208 GLN Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 307 LEU Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain b residue 348 SER Chi-restraints excluded: chain c residue 17 SER Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 65 ASN Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 212 ILE Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 228 THR Chi-restraints excluded: chain c residue 276 ASP Chi-restraints excluded: chain c residue 324 LEU Chi-restraints excluded: chain c residue 349 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 67 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 201 optimal weight: 10.0000 chunk 169 optimal weight: 20.0000 chunk 193 optimal weight: 10.0000 chunk 87 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 195 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 GLN a 48 ASN c 166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.201846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.132800 restraints weight = 16334.430| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.18 r_work: 0.3261 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16544 Z= 0.144 Angle : 0.540 7.951 22462 Z= 0.285 Chirality : 0.043 0.133 2387 Planarity : 0.003 0.030 2862 Dihedral : 4.807 40.050 2168 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.29 % Favored : 94.66 % Rotamer: Outliers : 3.60 % Allowed : 17.38 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.19), residues: 2022 helix: 1.55 (0.36), residues: 223 sheet: -2.00 (0.23), residues: 491 loop : -1.01 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 41 TYR 0.018 0.001 TYR c 256 PHE 0.013 0.001 PHE B 277 TRP 0.014 0.001 TRP c 168 HIS 0.004 0.001 HIS b 293 Details of bonding type rmsd covalent geometry : bond 0.00347 (16514) covalent geometry : angle 0.53657 (22402) SS BOND : bond 0.00195 ( 30) SS BOND : angle 1.35933 ( 60) hydrogen bonds : bond 0.03632 ( 423) hydrogen bonds : angle 5.31099 ( 1086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 226 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7347 (m-90) cc_final: 0.6842 (p-90) REVERT: A 70 GLN cc_start: 0.7765 (tt0) cc_final: 0.7250 (tt0) REVERT: A 102 ARG cc_start: 0.7920 (mmm-85) cc_final: 0.7483 (mmt90) REVERT: A 272 LYS cc_start: 0.8875 (mttp) cc_final: 0.8438 (mtpm) REVERT: A 314 ARG cc_start: 0.7431 (ttp-170) cc_final: 0.7123 (ttm-80) REVERT: B 31 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7524 (mm-40) REVERT: B 70 GLN cc_start: 0.7423 (mt0) cc_final: 0.7078 (mp10) REVERT: B 89 VAL cc_start: 0.7230 (t) cc_final: 0.6646 (m) REVERT: B 142 GLU cc_start: 0.6638 (pt0) cc_final: 0.5978 (tm-30) REVERT: B 147 ARG cc_start: 0.8070 (mtp85) cc_final: 0.7742 (mtp85) REVERT: B 168 TRP cc_start: 0.7940 (m100) cc_final: 0.7656 (m100) REVERT: B 274 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7871 (tp30) REVERT: C 14 LYS cc_start: 0.8294 (tptm) cc_final: 0.7954 (tptp) REVERT: C 62 ARG cc_start: 0.7481 (ppt170) cc_final: 0.6962 (ttp-110) REVERT: C 74 GLU cc_start: 0.6642 (mt-10) cc_final: 0.6077 (mp0) REVERT: C 101 LYS cc_start: 0.7265 (mptt) cc_final: 0.6596 (mppt) REVERT: C 177 GLU cc_start: 0.7680 (mt-10) cc_final: 0.6909 (tt0) REVERT: C 214 LYS cc_start: 0.7746 (ptmm) cc_final: 0.7448 (pptt) REVERT: C 258 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.6594 (tm-30) REVERT: a 74 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6616 (mp0) REVERT: a 101 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.7921 (mttt) REVERT: a 214 LYS cc_start: 0.8690 (mtmt) cc_final: 0.7941 (mmmt) REVERT: a 287 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.7930 (mm) REVERT: a 314 ARG cc_start: 0.7005 (ttm170) cc_final: 0.6564 (ttm170) REVERT: b 96 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8182 (t) REVERT: b 147 ARG cc_start: 0.6811 (ptm160) cc_final: 0.6239 (mtm-85) REVERT: b 157 ASP cc_start: 0.8343 (p0) cc_final: 0.7905 (t0) REVERT: b 238 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7786 (mt-10) REVERT: c 154 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7205 (mt-10) REVERT: c 197 ASP cc_start: 0.8385 (p0) cc_final: 0.8052 (p0) REVERT: c 219 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8026 (pt0) REVERT: c 276 ASP cc_start: 0.8117 (m-30) cc_final: 0.7520 (m-30) REVERT: c 318 MET cc_start: 0.7729 (mpp) cc_final: 0.7472 (mpm) REVERT: c 340 GLU cc_start: 0.5028 (tp30) cc_final: 0.4686 (tp30) outliers start: 63 outliers final: 39 residues processed: 264 average time/residue: 0.6020 time to fit residues: 175.1833 Evaluate side-chains 264 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 217 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 101 LYS Chi-restraints excluded: chain a residue 208 GLN Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain a residue 344 ASN Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain b residue 177 GLU Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain b residue 348 SER Chi-restraints excluded: chain c residue 17 SER Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 212 ILE Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 219 GLU Chi-restraints excluded: chain c residue 262 THR Chi-restraints excluded: chain c residue 324 LEU Chi-restraints excluded: chain c residue 345 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 92 optimal weight: 1.9990 chunk 184 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 76 optimal weight: 0.4980 chunk 66 optimal weight: 0.0270 chunk 164 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.3044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN B 208 GLN c 166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.205032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.136472 restraints weight = 16298.255| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.93 r_work: 0.3341 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16544 Z= 0.113 Angle : 0.508 6.125 22462 Z= 0.267 Chirality : 0.042 0.132 2387 Planarity : 0.003 0.030 2862 Dihedral : 4.574 38.463 2168 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.59 % Favored : 94.36 % Rotamer: Outliers : 3.20 % Allowed : 18.64 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.19), residues: 2022 helix: 1.60 (0.37), residues: 224 sheet: -1.86 (0.23), residues: 487 loop : -0.87 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 41 TYR 0.019 0.001 TYR c 256 PHE 0.012 0.001 PHE B 277 TRP 0.015 0.001 TRP c 168 HIS 0.006 0.001 HIS b 293 Details of bonding type rmsd covalent geometry : bond 0.00266 (16514) covalent geometry : angle 0.50436 (22402) SS BOND : bond 0.00407 ( 30) SS BOND : angle 1.21331 ( 60) hydrogen bonds : bond 0.03213 ( 423) hydrogen bonds : angle 5.11113 ( 1086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 216 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7124 (m-90) cc_final: 0.6904 (m100) REVERT: A 70 GLN cc_start: 0.7328 (tt0) cc_final: 0.6836 (tt0) REVERT: A 146 GLU cc_start: 0.7927 (mp0) cc_final: 0.7351 (mp0) REVERT: A 272 LYS cc_start: 0.8757 (mttp) cc_final: 0.8242 (mtpm) REVERT: A 347 LYS cc_start: 0.8616 (ptpp) cc_final: 0.7931 (pttt) REVERT: B 31 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7396 (mm-40) REVERT: B 70 GLN cc_start: 0.7274 (mt0) cc_final: 0.6899 (mp10) REVERT: B 89 VAL cc_start: 0.6921 (t) cc_final: 0.6363 (m) REVERT: B 142 GLU cc_start: 0.6637 (pt0) cc_final: 0.5992 (tm-30) REVERT: B 147 ARG cc_start: 0.7964 (mtp85) cc_final: 0.7610 (mtp85) REVERT: B 154 GLU cc_start: 0.7808 (pt0) cc_final: 0.7480 (pt0) REVERT: B 274 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7508 (tp30) REVERT: B 310 GLN cc_start: 0.6268 (OUTLIER) cc_final: 0.5937 (mp10) REVERT: C 14 LYS cc_start: 0.8101 (tptm) cc_final: 0.7744 (tptp) REVERT: C 62 ARG cc_start: 0.7203 (ppt170) cc_final: 0.6591 (ttp-110) REVERT: C 74 GLU cc_start: 0.6488 (mt-10) cc_final: 0.5932 (mp0) REVERT: C 101 LYS cc_start: 0.7044 (mptt) cc_final: 0.6624 (mppt) REVERT: C 177 GLU cc_start: 0.7463 (mt-10) cc_final: 0.6716 (tt0) REVERT: C 214 LYS cc_start: 0.7570 (ptmm) cc_final: 0.7174 (pptt) REVERT: C 258 GLN cc_start: 0.7208 (OUTLIER) cc_final: 0.6389 (tm-30) REVERT: a 74 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6293 (mp0) REVERT: a 214 LYS cc_start: 0.8586 (mtmt) cc_final: 0.8231 (mtpp) REVERT: a 287 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.7916 (mm) REVERT: a 314 ARG cc_start: 0.6895 (ttm170) cc_final: 0.6452 (ttm170) REVERT: b 147 ARG cc_start: 0.6632 (ptm160) cc_final: 0.6059 (mtm-85) REVERT: b 157 ASP cc_start: 0.8135 (p0) cc_final: 0.7684 (t0) REVERT: c 154 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6841 (mt-10) REVERT: c 156 GLU cc_start: 0.7985 (pt0) cc_final: 0.7413 (tt0) REVERT: c 197 ASP cc_start: 0.8161 (p0) cc_final: 0.7789 (p0) REVERT: c 219 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7801 (pt0) REVERT: c 228 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.7863 (t) REVERT: c 276 ASP cc_start: 0.7971 (m-30) cc_final: 0.7229 (m-30) REVERT: c 318 MET cc_start: 0.7593 (mpp) cc_final: 0.7335 (mpm) REVERT: c 340 GLU cc_start: 0.4916 (tp30) cc_final: 0.4597 (tp30) outliers start: 56 outliers final: 39 residues processed: 247 average time/residue: 0.5734 time to fit residues: 156.7739 Evaluate side-chains 256 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 210 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 310 GLN Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 208 GLN Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain a residue 344 ASN Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 177 GLU Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain c residue 17 SER Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 65 ASN Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 212 ILE Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 219 GLU Chi-restraints excluded: chain c residue 228 THR Chi-restraints excluded: chain c residue 241 MET Chi-restraints excluded: chain c residue 262 THR Chi-restraints excluded: chain c residue 324 LEU Chi-restraints excluded: chain c residue 345 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 106 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 28 optimal weight: 0.2980 chunk 195 optimal weight: 0.3980 chunk 87 optimal weight: 3.9990 chunk 178 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 83 optimal weight: 0.1980 chunk 187 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 GLN a 48 ASN a 269 HIS b 293 HIS c 166 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.204583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.135829 restraints weight = 16402.755| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.88 r_work: 0.3343 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16544 Z= 0.096 Angle : 0.497 7.785 22462 Z= 0.260 Chirality : 0.041 0.132 2387 Planarity : 0.003 0.042 2862 Dihedral : 4.371 34.522 2168 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.90 % Favored : 95.05 % Rotamer: Outliers : 2.74 % Allowed : 19.73 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.19), residues: 2022 helix: 1.62 (0.37), residues: 224 sheet: -1.80 (0.23), residues: 493 loop : -0.74 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 41 TYR 0.018 0.001 TYR c 256 PHE 0.012 0.001 PHE B 277 TRP 0.015 0.001 TRP c 168 HIS 0.006 0.001 HIS b 293 Details of bonding type rmsd covalent geometry : bond 0.00224 (16514) covalent geometry : angle 0.49435 (22402) SS BOND : bond 0.00176 ( 30) SS BOND : angle 1.07244 ( 60) hydrogen bonds : bond 0.02918 ( 423) hydrogen bonds : angle 4.97389 ( 1086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 226 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7195 (m-90) cc_final: 0.6977 (m100) REVERT: A 70 GLN cc_start: 0.7543 (tt0) cc_final: 0.7036 (tt0) REVERT: A 146 GLU cc_start: 0.7973 (mp0) cc_final: 0.7406 (mp0) REVERT: A 272 LYS cc_start: 0.8782 (mttp) cc_final: 0.8328 (mtpm) REVERT: A 347 LYS cc_start: 0.8597 (ptpp) cc_final: 0.7916 (pttt) REVERT: B 70 GLN cc_start: 0.7355 (mt0) cc_final: 0.6955 (mp10) REVERT: B 76 ASN cc_start: 0.6260 (m-40) cc_final: 0.5987 (m110) REVERT: B 89 VAL cc_start: 0.7116 (t) cc_final: 0.6598 (m) REVERT: B 142 GLU cc_start: 0.6712 (pt0) cc_final: 0.5963 (pp20) REVERT: B 147 ARG cc_start: 0.8087 (mtp85) cc_final: 0.7772 (mtp85) REVERT: B 154 GLU cc_start: 0.7915 (pt0) cc_final: 0.7623 (pt0) REVERT: B 274 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7663 (tp30) REVERT: B 310 GLN cc_start: 0.6259 (OUTLIER) cc_final: 0.5858 (mp10) REVERT: C 14 LYS cc_start: 0.8130 (tptm) cc_final: 0.7765 (tptp) REVERT: C 62 ARG cc_start: 0.7281 (ppt170) cc_final: 0.6691 (ttp-110) REVERT: C 74 GLU cc_start: 0.6568 (mt-10) cc_final: 0.6033 (mp0) REVERT: C 101 LYS cc_start: 0.7069 (mptt) cc_final: 0.6666 (mppt) REVERT: C 177 GLU cc_start: 0.7548 (mt-10) cc_final: 0.6818 (tt0) REVERT: C 214 LYS cc_start: 0.7633 (ptmm) cc_final: 0.7186 (pptt) REVERT: C 258 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6368 (tm-30) REVERT: a 74 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6364 (mp0) REVERT: a 214 LYS cc_start: 0.8584 (mtmt) cc_final: 0.8280 (mtpp) REVERT: a 287 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8064 (mm) REVERT: a 314 ARG cc_start: 0.7003 (ttm170) cc_final: 0.6569 (ttm170) REVERT: b 96 VAL cc_start: 0.8508 (OUTLIER) cc_final: 0.8088 (t) REVERT: b 147 ARG cc_start: 0.6704 (ptm160) cc_final: 0.6115 (mtm-85) REVERT: b 157 ASP cc_start: 0.8207 (p0) cc_final: 0.7848 (t0) REVERT: c 154 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7050 (mt-10) REVERT: c 156 GLU cc_start: 0.8014 (pt0) cc_final: 0.7524 (tt0) REVERT: c 197 ASP cc_start: 0.8150 (p0) cc_final: 0.7833 (p0) REVERT: c 219 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7805 (pt0) REVERT: c 228 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8040 (t) REVERT: c 276 ASP cc_start: 0.8064 (m-30) cc_final: 0.7376 (m-30) REVERT: c 318 MET cc_start: 0.7596 (mpp) cc_final: 0.7346 (mpm) outliers start: 48 outliers final: 32 residues processed: 254 average time/residue: 0.5605 time to fit residues: 157.5677 Evaluate side-chains 255 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 216 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 310 GLN Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain b residue 148 ARG Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 65 ASN Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 212 ILE Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 219 GLU Chi-restraints excluded: chain c residue 228 THR Chi-restraints excluded: chain c residue 241 MET Chi-restraints excluded: chain c residue 324 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 51 optimal weight: 0.6980 chunk 186 optimal weight: 6.9990 chunk 150 optimal weight: 0.4980 chunk 174 optimal weight: 20.0000 chunk 176 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 GLN a 35 GLN a 48 ASN a 344 ASN b 293 HIS c 166 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.204978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.136523 restraints weight = 16350.579| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.81 r_work: 0.3338 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16544 Z= 0.099 Angle : 0.497 7.526 22462 Z= 0.260 Chirality : 0.042 0.132 2387 Planarity : 0.003 0.030 2862 Dihedral : 4.283 30.578 2168 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.19 % Favored : 94.76 % Rotamer: Outliers : 2.74 % Allowed : 20.01 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.19), residues: 2022 helix: 1.64 (0.37), residues: 224 sheet: -1.75 (0.23), residues: 497 loop : -0.70 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 41 TYR 0.018 0.001 TYR c 256 PHE 0.012 0.001 PHE c 277 TRP 0.014 0.001 TRP c 168 HIS 0.008 0.001 HIS b 293 Details of bonding type rmsd covalent geometry : bond 0.00231 (16514) covalent geometry : angle 0.49476 (22402) SS BOND : bond 0.00185 ( 30) SS BOND : angle 1.03670 ( 60) hydrogen bonds : bond 0.02934 ( 423) hydrogen bonds : angle 4.95638 ( 1086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 219 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7719 (tt0) cc_final: 0.7242 (tt0) REVERT: A 146 GLU cc_start: 0.8024 (mp0) cc_final: 0.7474 (mp0) REVERT: A 347 LYS cc_start: 0.8596 (ptpp) cc_final: 0.8007 (pttt) REVERT: B 70 GLN cc_start: 0.7386 (mt0) cc_final: 0.7059 (mp10) REVERT: B 76 ASN cc_start: 0.6303 (m-40) cc_final: 0.6032 (m110) REVERT: B 89 VAL cc_start: 0.7255 (t) cc_final: 0.6755 (m) REVERT: B 142 GLU cc_start: 0.6661 (pt0) cc_final: 0.5998 (pp20) REVERT: B 147 ARG cc_start: 0.8226 (mtp85) cc_final: 0.7869 (mtp85) REVERT: B 154 GLU cc_start: 0.7997 (pt0) cc_final: 0.7712 (pt0) REVERT: B 213 GLU cc_start: 0.8418 (tt0) cc_final: 0.8107 (pt0) REVERT: B 274 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7776 (tp30) REVERT: C 14 LYS cc_start: 0.8198 (tptm) cc_final: 0.7831 (tptp) REVERT: C 74 GLU cc_start: 0.6581 (mt-10) cc_final: 0.6029 (mp0) REVERT: C 101 LYS cc_start: 0.7176 (mptt) cc_final: 0.6796 (mppt) REVERT: C 177 GLU cc_start: 0.7610 (mt-10) cc_final: 0.6918 (tt0) REVERT: C 214 LYS cc_start: 0.7717 (ptmm) cc_final: 0.7302 (pptt) REVERT: C 258 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6285 (tm-30) REVERT: C 314 ARG cc_start: 0.5142 (ttm170) cc_final: 0.4653 (ttm170) REVERT: a 214 LYS cc_start: 0.8576 (mtmt) cc_final: 0.8311 (mtpp) REVERT: a 287 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8089 (mm) REVERT: a 314 ARG cc_start: 0.7058 (ttm170) cc_final: 0.6638 (ttm170) REVERT: b 50 HIS cc_start: 0.7204 (t-90) cc_final: 0.6982 (t-90) REVERT: b 147 ARG cc_start: 0.6908 (ptm160) cc_final: 0.6264 (mtm-85) REVERT: b 157 ASP cc_start: 0.8250 (p0) cc_final: 0.7943 (t0) REVERT: c 154 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7168 (mt-10) REVERT: c 156 GLU cc_start: 0.8042 (pt0) cc_final: 0.7593 (tt0) REVERT: c 197 ASP cc_start: 0.8180 (p0) cc_final: 0.7880 (p0) REVERT: c 228 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8148 (t) REVERT: c 276 ASP cc_start: 0.8127 (m-30) cc_final: 0.7475 (m-30) REVERT: c 318 MET cc_start: 0.7645 (mpp) cc_final: 0.7406 (mpm) outliers start: 48 outliers final: 35 residues processed: 247 average time/residue: 0.5603 time to fit residues: 153.5346 Evaluate side-chains 253 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 148 ARG Chi-restraints excluded: chain b residue 177 GLU Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 65 ASN Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 212 ILE Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 228 THR Chi-restraints excluded: chain c residue 241 MET Chi-restraints excluded: chain c residue 324 LEU Chi-restraints excluded: chain c residue 345 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 96 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 189 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 GLN b 293 HIS c 166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.201713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.134214 restraints weight = 16307.415| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.74 r_work: 0.3335 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16544 Z= 0.174 Angle : 0.559 7.999 22462 Z= 0.292 Chirality : 0.043 0.137 2387 Planarity : 0.003 0.053 2862 Dihedral : 4.586 31.531 2168 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.98 % Favored : 93.97 % Rotamer: Outliers : 2.69 % Allowed : 20.47 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.19), residues: 2022 helix: 1.60 (0.37), residues: 224 sheet: -1.81 (0.23), residues: 491 loop : -0.84 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 41 TYR 0.017 0.001 TYR A 256 PHE 0.014 0.002 PHE c 34 TRP 0.015 0.001 TRP c 168 HIS 0.008 0.001 HIS b 293 Details of bonding type rmsd covalent geometry : bond 0.00425 (16514) covalent geometry : angle 0.55730 (22402) SS BOND : bond 0.00221 ( 30) SS BOND : angle 1.08775 ( 60) hydrogen bonds : bond 0.03799 ( 423) hydrogen bonds : angle 5.14225 ( 1086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 210 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7511 (tt0) cc_final: 0.7021 (tt0) REVERT: A 102 ARG cc_start: 0.7755 (mmm-85) cc_final: 0.7307 (mmt90) REVERT: A 146 GLU cc_start: 0.7965 (mp0) cc_final: 0.7296 (mp0) REVERT: A 314 ARG cc_start: 0.7303 (ttp-170) cc_final: 0.7024 (ttm-80) REVERT: A 347 LYS cc_start: 0.8665 (ptpp) cc_final: 0.7979 (pttt) REVERT: B 70 GLN cc_start: 0.7308 (mt0) cc_final: 0.6986 (mp10) REVERT: B 89 VAL cc_start: 0.7105 (t) cc_final: 0.6576 (m) REVERT: B 142 GLU cc_start: 0.6732 (pt0) cc_final: 0.6095 (pp20) REVERT: B 147 ARG cc_start: 0.8108 (mtp85) cc_final: 0.7831 (mtp85) REVERT: B 154 GLU cc_start: 0.7904 (pt0) cc_final: 0.7627 (pt0) REVERT: B 238 GLU cc_start: 0.7991 (mt-10) cc_final: 0.6738 (pm20) REVERT: B 274 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7619 (tp30) REVERT: C 14 LYS cc_start: 0.8182 (tptm) cc_final: 0.7821 (tptp) REVERT: C 62 ARG cc_start: 0.7324 (ppt170) cc_final: 0.7020 (ttp80) REVERT: C 74 GLU cc_start: 0.6543 (mt-10) cc_final: 0.6007 (mp0) REVERT: C 101 LYS cc_start: 0.7168 (mptt) cc_final: 0.6740 (mppt) REVERT: C 177 GLU cc_start: 0.7531 (mt-10) cc_final: 0.6771 (tt0) REVERT: C 197 ASP cc_start: 0.8135 (p0) cc_final: 0.7921 (p0) REVERT: C 214 LYS cc_start: 0.7569 (ptmm) cc_final: 0.7100 (pptt) REVERT: C 258 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6244 (tm-30) REVERT: a 74 GLU cc_start: 0.7207 (tt0) cc_final: 0.6823 (mp0) REVERT: a 214 LYS cc_start: 0.8617 (mtmt) cc_final: 0.8290 (mtpp) REVERT: a 276 ASP cc_start: 0.8338 (p0) cc_final: 0.8097 (p0) REVERT: a 287 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.7964 (mm) REVERT: a 314 ARG cc_start: 0.6946 (ttm170) cc_final: 0.6506 (ttm170) REVERT: b 50 HIS cc_start: 0.7102 (t-90) cc_final: 0.6872 (t-90) REVERT: b 96 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8107 (t) REVERT: b 147 ARG cc_start: 0.6642 (ptm160) cc_final: 0.6071 (mtm-85) REVERT: b 157 ASP cc_start: 0.8172 (p0) cc_final: 0.7777 (t0) REVERT: b 238 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7615 (mt-10) REVERT: c 156 GLU cc_start: 0.8022 (pt0) cc_final: 0.7534 (tt0) REVERT: c 197 ASP cc_start: 0.8364 (p0) cc_final: 0.8040 (p0) REVERT: c 276 ASP cc_start: 0.8015 (m-30) cc_final: 0.7329 (m-30) REVERT: c 318 MET cc_start: 0.7639 (mpp) cc_final: 0.7380 (mpm) outliers start: 47 outliers final: 38 residues processed: 238 average time/residue: 0.5943 time to fit residues: 156.1539 Evaluate side-chains 250 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 208 GLN Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain b residue 148 ARG Chi-restraints excluded: chain b residue 177 GLU Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 65 ASN Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 212 ILE Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 228 THR Chi-restraints excluded: chain c residue 262 THR Chi-restraints excluded: chain c residue 324 LEU Chi-restraints excluded: chain c residue 345 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 93 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 43 optimal weight: 0.0370 chunk 140 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN B 208 GLN c 166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.204697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.136547 restraints weight = 16219.307| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.78 r_work: 0.3295 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16544 Z= 0.097 Angle : 0.501 7.392 22462 Z= 0.262 Chirality : 0.042 0.133 2387 Planarity : 0.003 0.052 2862 Dihedral : 4.319 27.507 2168 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.09 % Favored : 94.86 % Rotamer: Outliers : 2.23 % Allowed : 21.04 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.19), residues: 2022 helix: 1.62 (0.37), residues: 224 sheet: -1.74 (0.23), residues: 497 loop : -0.69 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 41 TYR 0.018 0.001 TYR c 256 PHE 0.012 0.001 PHE a 277 TRP 0.013 0.001 TRP c 168 HIS 0.007 0.001 HIS b 293 Details of bonding type rmsd covalent geometry : bond 0.00226 (16514) covalent geometry : angle 0.49944 (22402) SS BOND : bond 0.00179 ( 30) SS BOND : angle 1.00652 ( 60) hydrogen bonds : bond 0.02915 ( 423) hydrogen bonds : angle 4.97015 ( 1086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6329.65 seconds wall clock time: 108 minutes 10.84 seconds (6490.84 seconds total)