Starting phenix.real_space_refine on Sat Aug 23 13:03:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f35_28832/08_2025/8f35_28832.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f35_28832/08_2025/8f35_28832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8f35_28832/08_2025/8f35_28832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f35_28832/08_2025/8f35_28832.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f35_28832/08_2025/8f35_28832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f35_28832/08_2025/8f35_28832.map" } resolution = 3.17 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= 0.000 sd= 0.014 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 30 5.16 5 C 8165 2.51 5 N 2080 2.21 5 O 2250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 12525 Number of models: 1 Model: "" Number of chains: 1 Chain: "E" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Restraints were copied for chains: D, C, B, A Time building chain proxies: 2.16, per 1000 atoms: 0.17 Number of scatterers: 12525 At special positions: 0 Unit cell: (89.352, 90.009, 123.516, 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 30 16.00 O 2250 8.00 N 2080 7.00 C 8165 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.01 Conformation dependent library (CDL) restraints added in 515.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 38.1% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'E' and resid 61 through 70 removed outlier: 3.875A pdb=" N ARG E 65 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 177 through 182 removed outlier: 4.276A pdb=" N VAL E 181 " --> pdb=" O HIS E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 208 Processing helix chain 'E' and resid 208 through 221 removed outlier: 3.654A pdb=" N LEU E 212 " --> pdb=" O PHE E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 225 removed outlier: 3.558A pdb=" N LEU E 225 " --> pdb=" O VAL E 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 222 through 225' Processing helix chain 'E' and resid 227 through 251 removed outlier: 3.765A pdb=" N PHE E 247 " --> pdb=" O VAL E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 285 Processing helix chain 'E' and resid 296 through 300 removed outlier: 3.502A pdb=" N CYS E 300 " --> pdb=" O ILE E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 317 removed outlier: 3.556A pdb=" N ILE E 317 " --> pdb=" O CYS E 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 70 removed outlier: 3.876A pdb=" N ARG D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 177 through 182 removed outlier: 4.276A pdb=" N VAL D 181 " --> pdb=" O HIS D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 208 through 221 removed outlier: 3.655A pdb=" N LEU D 212 " --> pdb=" O PHE D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 removed outlier: 3.558A pdb=" N LEU D 225 " --> pdb=" O VAL D 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 222 through 225' Processing helix chain 'D' and resid 227 through 251 removed outlier: 3.765A pdb=" N PHE D 247 " --> pdb=" O VAL D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 285 Processing helix chain 'D' and resid 296 through 300 removed outlier: 3.503A pdb=" N CYS D 300 " --> pdb=" O ILE D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 317 removed outlier: 3.555A pdb=" N ILE D 317 " --> pdb=" O CYS D 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 70 removed outlier: 3.874A pdb=" N ARG C 65 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 177 through 182 removed outlier: 4.276A pdb=" N VAL C 181 " --> pdb=" O HIS C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 208 through 221 removed outlier: 3.655A pdb=" N LEU C 212 " --> pdb=" O PHE C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 225 removed outlier: 3.558A pdb=" N LEU C 225 " --> pdb=" O VAL C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 222 through 225' Processing helix chain 'C' and resid 227 through 251 removed outlier: 3.765A pdb=" N PHE C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 285 Processing helix chain 'C' and resid 296 through 300 removed outlier: 3.501A pdb=" N CYS C 300 " --> pdb=" O ILE C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 317 removed outlier: 3.556A pdb=" N ILE C 317 " --> pdb=" O CYS C 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 70 removed outlier: 3.875A pdb=" N ARG B 65 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 177 through 182 removed outlier: 4.276A pdb=" N VAL B 181 " --> pdb=" O HIS B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 208 Processing helix chain 'B' and resid 208 through 221 removed outlier: 3.655A pdb=" N LEU B 212 " --> pdb=" O PHE B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 225 removed outlier: 3.558A pdb=" N LEU B 225 " --> pdb=" O VAL B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 222 through 225' Processing helix chain 'B' and resid 227 through 251 removed outlier: 3.765A pdb=" N PHE B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 285 Processing helix chain 'B' and resid 296 through 300 removed outlier: 3.502A pdb=" N CYS B 300 " --> pdb=" O ILE B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 317 removed outlier: 3.555A pdb=" N ILE B 317 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 70 removed outlier: 3.876A pdb=" N ARG A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 177 through 182 removed outlier: 4.276A pdb=" N VAL A 181 " --> pdb=" O HIS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 208 through 221 removed outlier: 3.655A pdb=" N LEU A 212 " --> pdb=" O PHE A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 removed outlier: 3.558A pdb=" N LEU A 225 " --> pdb=" O VAL A 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 222 through 225' Processing helix chain 'A' and resid 227 through 251 removed outlier: 3.765A pdb=" N PHE A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 285 Processing helix chain 'A' and resid 296 through 300 removed outlier: 3.503A pdb=" N CYS A 300 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 317 removed outlier: 3.555A pdb=" N ILE A 317 " --> pdb=" O CYS A 313 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 56 through 58 removed outlier: 6.687A pdb=" N THR E 32 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL E 26 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS E 22 " --> pdb=" O ASP E 36 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR E 38 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ILE E 20 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL E 40 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE E 18 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLN E 42 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N VAL E 16 " --> pdb=" O GLN E 42 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N THR E 44 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL E 14 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL E 12 " --> pdb=" O ARG E 141 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER E 143 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL E 14 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE E 145 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL E 16 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL E 147 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE E 18 " --> pdb=" O VAL E 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.672A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE E 188 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER E 171 " --> pdb=" O PHE E 188 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG E 190 " --> pdb=" O HIS E 169 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS E 169 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR E 192 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N SER E 167 " --> pdb=" O THR E 192 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG E 194 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LYS E 165 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP E 196 " --> pdb=" O ARG E 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 56 through 58 removed outlier: 6.687A pdb=" N THR D 32 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL D 26 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS D 22 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR D 38 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ILE D 20 " --> pdb=" O TYR D 38 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL D 40 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE D 18 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLN D 42 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N VAL D 16 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N THR D 44 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL D 14 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL D 12 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER D 143 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N VAL D 14 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE D 145 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL D 16 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL D 147 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE D 18 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.672A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE D 188 " --> pdb=" O SER D 171 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER D 171 " --> pdb=" O PHE D 188 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG D 190 " --> pdb=" O HIS D 169 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS D 169 " --> pdb=" O ARG D 190 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR D 192 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N SER D 167 " --> pdb=" O THR D 192 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG D 194 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LYS D 165 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP D 196 " --> pdb=" O ARG D 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 56 through 58 removed outlier: 6.688A pdb=" N THR C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL C 26 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS C 22 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR C 38 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ILE C 20 " --> pdb=" O TYR C 38 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL C 40 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE C 18 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLN C 42 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL C 16 " --> pdb=" O GLN C 42 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N THR C 44 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL C 14 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL C 12 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER C 143 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL C 14 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE C 145 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL C 16 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL C 147 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE C 18 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.672A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE C 188 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER C 171 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG C 190 " --> pdb=" O HIS C 169 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N HIS C 169 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR C 192 " --> pdb=" O SER C 167 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N SER C 167 " --> pdb=" O THR C 192 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG C 194 " --> pdb=" O LYS C 165 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LYS C 165 " --> pdb=" O ARG C 194 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASP C 196 " --> pdb=" O ARG C 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 56 through 58 removed outlier: 6.687A pdb=" N THR B 32 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL B 26 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B 22 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR B 38 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ILE B 20 " --> pdb=" O TYR B 38 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL B 40 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE B 18 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLN B 42 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL B 16 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N THR B 44 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL B 14 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL B 12 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER B 143 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL B 14 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE B 145 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL B 16 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL B 147 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE B 18 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.672A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE B 188 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER B 171 " --> pdb=" O PHE B 188 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG B 190 " --> pdb=" O HIS B 169 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS B 169 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR B 192 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N SER B 167 " --> pdb=" O THR B 192 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG B 194 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LYS B 165 " --> pdb=" O ARG B 194 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP B 196 " --> pdb=" O ARG B 163 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.687A pdb=" N THR A 32 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL A 26 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS A 22 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR A 38 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ILE A 20 " --> pdb=" O TYR A 38 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL A 40 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE A 18 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLN A 42 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N VAL A 16 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N THR A 44 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL A 14 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL A 12 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER A 143 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N VAL A 14 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A 145 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL A 16 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL A 147 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE A 18 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.672A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE A 188 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER A 171 " --> pdb=" O PHE A 188 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG A 190 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS A 169 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR A 192 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N SER A 167 " --> pdb=" O THR A 192 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG A 194 " --> pdb=" O LYS A 165 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LYS A 165 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP A 196 " --> pdb=" O ARG A 163 " (cutoff:3.500A) 540 hydrogen bonds defined for protein. 1575 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: 2.11 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3131 1.33 - 1.45: 2671 1.45 - 1.57: 7013 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 12865 Sorted by residual: bond pdb=" CA ILE C 157 " pdb=" C ILE C 157 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.27e-02 6.20e+03 5.17e+00 bond pdb=" CA ILE A 157 " pdb=" C ILE A 157 " ideal model delta sigma weight residual 1.523 1.495 0.028 1.27e-02 6.20e+03 4.86e+00 bond pdb=" CA ILE D 157 " pdb=" C ILE D 157 " ideal model delta sigma weight residual 1.523 1.495 0.028 1.27e-02 6.20e+03 4.77e+00 bond pdb=" CA ILE E 157 " pdb=" C ILE E 157 " ideal model delta sigma weight residual 1.523 1.495 0.028 1.27e-02 6.20e+03 4.72e+00 bond pdb=" CA ILE B 157 " pdb=" C ILE B 157 " ideal model delta sigma weight residual 1.523 1.496 0.027 1.27e-02 6.20e+03 4.61e+00 ... (remaining 12860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 16493 1.33 - 2.66: 812 2.66 - 3.99: 135 3.99 - 5.31: 60 5.31 - 6.64: 35 Bond angle restraints: 17535 Sorted by residual: angle pdb=" N VAL B 291 " pdb=" CA VAL B 291 " pdb=" C VAL B 291 " ideal model delta sigma weight residual 113.53 109.61 3.92 9.80e-01 1.04e+00 1.60e+01 angle pdb=" N VAL D 291 " pdb=" CA VAL D 291 " pdb=" C VAL D 291 " ideal model delta sigma weight residual 113.53 109.62 3.91 9.80e-01 1.04e+00 1.59e+01 angle pdb=" N VAL E 291 " pdb=" CA VAL E 291 " pdb=" C VAL E 291 " ideal model delta sigma weight residual 113.53 109.62 3.91 9.80e-01 1.04e+00 1.59e+01 angle pdb=" N VAL A 291 " pdb=" CA VAL A 291 " pdb=" C VAL A 291 " ideal model delta sigma weight residual 113.53 109.63 3.90 9.80e-01 1.04e+00 1.59e+01 angle pdb=" N VAL C 291 " pdb=" CA VAL C 291 " pdb=" C VAL C 291 " ideal model delta sigma weight residual 113.53 109.66 3.87 9.80e-01 1.04e+00 1.56e+01 ... (remaining 17530 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 6727 16.75 - 33.51: 618 33.51 - 50.26: 130 50.26 - 67.02: 25 67.02 - 83.77: 25 Dihedral angle restraints: 7525 sinusoidal: 3020 harmonic: 4505 Sorted by residual: dihedral pdb=" CA ARG A 117 " pdb=" C ARG A 117 " pdb=" N LEU A 118 " pdb=" CA LEU A 118 " ideal model delta harmonic sigma weight residual -180.00 -163.49 -16.51 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ARG D 117 " pdb=" C ARG D 117 " pdb=" N LEU D 118 " pdb=" CA LEU D 118 " ideal model delta harmonic sigma weight residual 180.00 -163.51 -16.49 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ARG B 117 " pdb=" C ARG B 117 " pdb=" N LEU B 118 " pdb=" CA LEU B 118 " ideal model delta harmonic sigma weight residual 180.00 -163.51 -16.49 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 7522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1003 0.032 - 0.065: 578 0.065 - 0.097: 200 0.097 - 0.129: 143 0.129 - 0.161: 26 Chirality restraints: 1950 Sorted by residual: chirality pdb=" CB ILE D 145 " pdb=" CA ILE D 145 " pdb=" CG1 ILE D 145 " pdb=" CG2 ILE D 145 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CB ILE A 145 " pdb=" CA ILE A 145 " pdb=" CG1 ILE A 145 " pdb=" CG2 ILE A 145 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" CB ILE E 145 " pdb=" CA ILE E 145 " pdb=" CG1 ILE E 145 " pdb=" CG2 ILE E 145 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.32e-01 ... (remaining 1947 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 255 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.34e+00 pdb=" C ARG B 255 " 0.040 2.00e-02 2.50e+03 pdb=" O ARG B 255 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU B 256 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 255 " -0.012 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C ARG D 255 " 0.040 2.00e-02 2.50e+03 pdb=" O ARG D 255 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU D 256 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 255 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.23e+00 pdb=" C ARG E 255 " 0.040 2.00e-02 2.50e+03 pdb=" O ARG E 255 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU E 256 " -0.013 2.00e-02 2.50e+03 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2156 2.77 - 3.30: 11455 3.30 - 3.83: 21643 3.83 - 4.37: 25522 4.37 - 4.90: 43725 Nonbonded interactions: 104501 Sorted by model distance: nonbonded pdb=" NH2 ARG E 105 " pdb=" O VAL D 81 " model vdw 2.235 3.120 nonbonded pdb=" N PHE C 116 " pdb=" OH TYR C 258 " model vdw 2.243 3.120 nonbonded pdb=" N PHE E 116 " pdb=" OH TYR E 258 " model vdw 2.243 3.120 nonbonded pdb=" N PHE D 116 " pdb=" OH TYR D 258 " model vdw 2.243 3.120 nonbonded pdb=" N PHE B 116 " pdb=" OH TYR B 258 " model vdw 2.243 3.120 ... (remaining 104496 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: 0.02 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'C' selection = chain 'B' selection = chain 'A' } 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: 1.320 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.690 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12865 Z= 0.245 Angle : 0.746 6.643 17535 Z= 0.428 Chirality : 0.051 0.161 1950 Planarity : 0.005 0.037 2235 Dihedral : 14.231 83.771 4615 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.03 (0.21), residues: 1525 helix: 0.08 (0.22), residues: 510 sheet: 0.45 (0.23), residues: 485 loop : -2.55 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 99 TYR 0.020 0.002 TYR C 270 PHE 0.017 0.002 PHE C 236 TRP 0.009 0.001 TRP A 72 HIS 0.008 0.002 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00491 (12865) covalent geometry : angle 0.74558 (17535) hydrogen bonds : bond 0.12249 ( 540) hydrogen bonds : angle 5.86554 ( 1575) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.472 Fit side-chains REVERT: D 13 ASP cc_start: 0.6885 (m-30) cc_final: 0.6428 (m-30) REVERT: C 122 ASP cc_start: 0.7345 (m-30) cc_final: 0.6955 (m-30) REVERT: A 204 TYR cc_start: 0.8073 (m-80) cc_final: 0.7700 (m-80) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1180 time to fit residues: 39.2160 Evaluate side-chains 189 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.0070 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.0470 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.1700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 60 ASN E 285 HIS D 60 ASN D 169 HIS C 60 ASN C 169 HIS B 60 ASN B 169 HIS A 60 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.158807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.130347 restraints weight = 13207.976| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.82 r_work: 0.3186 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12865 Z= 0.120 Angle : 0.488 4.840 17535 Z= 0.261 Chirality : 0.044 0.153 1950 Planarity : 0.004 0.030 2235 Dihedral : 4.456 16.302 1685 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.51 % Allowed : 6.98 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.32 (0.21), residues: 1525 helix: 1.39 (0.23), residues: 505 sheet: 0.25 (0.23), residues: 500 loop : -2.33 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 105 TYR 0.011 0.001 TYR A 270 PHE 0.011 0.001 PHE C 236 TRP 0.009 0.001 TRP E 161 HIS 0.003 0.001 HIS D 285 Details of bonding type rmsd covalent geometry : bond 0.00274 (12865) covalent geometry : angle 0.48838 (17535) hydrogen bonds : bond 0.03394 ( 540) hydrogen bonds : angle 4.50719 ( 1575) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 219 time to evaluate : 0.530 Fit side-chains REVERT: E 114 MET cc_start: 0.8499 (mtm) cc_final: 0.8289 (mtp) REVERT: E 255 ARG cc_start: 0.7880 (mmp80) cc_final: 0.6861 (mmt90) REVERT: E 258 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7451 (p90) REVERT: C 114 MET cc_start: 0.8391 (mtm) cc_final: 0.8086 (mtp) REVERT: A 114 MET cc_start: 0.8384 (mtm) cc_final: 0.8083 (mtp) outliers start: 7 outliers final: 6 residues processed: 224 average time/residue: 0.1124 time to fit residues: 36.5566 Evaluate side-chains 203 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 196 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain A residue 167 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 143 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 17 optimal weight: 0.0270 chunk 88 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 63 optimal weight: 0.1980 chunk 128 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.2440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 169 HIS C 169 HIS B 169 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.155375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.125934 restraints weight = 13278.190| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.84 r_work: 0.3121 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12865 Z= 0.118 Angle : 0.483 5.040 17535 Z= 0.255 Chirality : 0.045 0.175 1950 Planarity : 0.004 0.028 2235 Dihedral : 4.391 14.776 1685 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.95 % Allowed : 8.80 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.06 (0.21), residues: 1525 helix: 1.78 (0.23), residues: 510 sheet: 0.31 (0.24), residues: 475 loop : -2.23 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 255 TYR 0.010 0.001 TYR A 270 PHE 0.013 0.001 PHE C 236 TRP 0.011 0.001 TRP E 161 HIS 0.003 0.001 HIS E 285 Details of bonding type rmsd covalent geometry : bond 0.00272 (12865) covalent geometry : angle 0.48335 (17535) hydrogen bonds : bond 0.03332 ( 540) hydrogen bonds : angle 4.31884 ( 1575) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 196 time to evaluate : 0.472 Fit side-chains REVERT: E 114 MET cc_start: 0.8524 (mtm) cc_final: 0.8322 (mtp) REVERT: E 255 ARG cc_start: 0.7772 (mmp80) cc_final: 0.6858 (mmt90) REVERT: E 258 TYR cc_start: 0.8348 (OUTLIER) cc_final: 0.7453 (p90) REVERT: D 59 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8270 (mm-30) REVERT: D 122 ASP cc_start: 0.7997 (m-30) cc_final: 0.7322 (m-30) REVERT: C 114 MET cc_start: 0.8502 (mtm) cc_final: 0.8293 (mtp) REVERT: C 150 GLU cc_start: 0.7050 (tt0) cc_final: 0.6841 (mt-10) REVERT: B 31 GLN cc_start: 0.8829 (mt0) cc_final: 0.8527 (mt0) REVERT: B 148 TYR cc_start: 0.8248 (m-80) cc_final: 0.7993 (m-80) REVERT: A 31 GLN cc_start: 0.8834 (mt0) cc_final: 0.8549 (mt0) REVERT: A 59 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8166 (mm-30) REVERT: A 114 MET cc_start: 0.8509 (mtm) cc_final: 0.8292 (mtp) outliers start: 13 outliers final: 6 residues processed: 203 average time/residue: 0.1240 time to fit residues: 36.1200 Evaluate side-chains 196 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 189 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain A residue 167 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 11 optimal weight: 8.9990 chunk 145 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 169 HIS E 251 ASN D 169 HIS D 251 ASN C 169 HIS B 169 HIS A 169 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.145576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.116850 restraints weight = 13562.346| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.50 r_work: 0.3025 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 12865 Z= 0.342 Angle : 0.718 6.525 17535 Z= 0.377 Chirality : 0.053 0.205 1950 Planarity : 0.005 0.034 2235 Dihedral : 5.572 21.977 1685 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 1.53 % Allowed : 12.07 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.45 (0.21), residues: 1525 helix: 1.19 (0.23), residues: 510 sheet: 0.10 (0.23), residues: 485 loop : -2.19 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 117 TYR 0.014 0.002 TYR B 270 PHE 0.023 0.003 PHE C 236 TRP 0.012 0.002 TRP A 206 HIS 0.005 0.001 HIS E 285 Details of bonding type rmsd covalent geometry : bond 0.00831 (12865) covalent geometry : angle 0.71838 (17535) hydrogen bonds : bond 0.05248 ( 540) hydrogen bonds : angle 4.84085 ( 1575) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.492 Fit side-chains REVERT: E 258 TYR cc_start: 0.8391 (OUTLIER) cc_final: 0.7407 (p90) REVERT: C 159 GLU cc_start: 0.7802 (tt0) cc_final: 0.7593 (tt0) REVERT: A 148 TYR cc_start: 0.8531 (m-80) cc_final: 0.8305 (m-80) REVERT: A 159 GLU cc_start: 0.7939 (tt0) cc_final: 0.7721 (tt0) outliers start: 21 outliers final: 19 residues processed: 156 average time/residue: 0.1328 time to fit residues: 29.4049 Evaluate side-chains 145 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 167 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 142 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 169 HIS D 169 HIS C 169 HIS B 169 HIS A 169 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.152434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.123157 restraints weight = 13407.852| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.51 r_work: 0.3125 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12865 Z= 0.109 Angle : 0.487 6.526 17535 Z= 0.258 Chirality : 0.044 0.148 1950 Planarity : 0.003 0.026 2235 Dihedral : 4.570 14.788 1685 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.31 % Allowed : 12.87 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.21), residues: 1525 helix: 1.92 (0.23), residues: 505 sheet: 0.19 (0.23), residues: 485 loop : -2.00 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 99 TYR 0.010 0.001 TYR C 270 PHE 0.012 0.001 PHE C 236 TRP 0.010 0.001 TRP E 161 HIS 0.003 0.001 HIS E 285 Details of bonding type rmsd covalent geometry : bond 0.00247 (12865) covalent geometry : angle 0.48697 (17535) hydrogen bonds : bond 0.03325 ( 540) hydrogen bonds : angle 4.35680 ( 1575) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.409 Fit side-chains REVERT: E 255 ARG cc_start: 0.7891 (mmp80) cc_final: 0.7654 (mmp80) REVERT: E 258 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.7282 (p90) REVERT: C 114 MET cc_start: 0.8474 (mtm) cc_final: 0.8224 (mtp) REVERT: B 247 PHE cc_start: 0.7323 (m-10) cc_final: 0.7092 (m-10) REVERT: B 255 ARG cc_start: 0.7794 (mmp80) cc_final: 0.6735 (mmt90) REVERT: A 114 MET cc_start: 0.8506 (mtm) cc_final: 0.8233 (mtp) REVERT: A 159 GLU cc_start: 0.7875 (tt0) cc_final: 0.7602 (tt0) outliers start: 18 outliers final: 15 residues processed: 195 average time/residue: 0.1339 time to fit residues: 36.3747 Evaluate side-chains 175 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 167 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 116 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 63 optimal weight: 0.3980 chunk 82 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 169 HIS D 169 HIS C 169 HIS B 169 HIS A 169 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.148820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.120745 restraints weight = 13454.425| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.68 r_work: 0.3080 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12865 Z= 0.183 Angle : 0.554 6.228 17535 Z= 0.292 Chirality : 0.047 0.194 1950 Planarity : 0.004 0.026 2235 Dihedral : 4.821 16.372 1685 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.89 % Allowed : 13.53 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.11 (0.21), residues: 1525 helix: 1.77 (0.23), residues: 505 sheet: 0.08 (0.23), residues: 485 loop : -2.06 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 105 TYR 0.013 0.001 TYR C 270 PHE 0.013 0.002 PHE C 236 TRP 0.012 0.001 TRP E 161 HIS 0.004 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00441 (12865) covalent geometry : angle 0.55430 (17535) hydrogen bonds : bond 0.04020 ( 540) hydrogen bonds : angle 4.46262 ( 1575) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.525 Fit side-chains REVERT: E 255 ARG cc_start: 0.7907 (mmp80) cc_final: 0.7620 (mmp80) REVERT: E 258 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7355 (p90) REVERT: D 122 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.8030 (m-30) REVERT: D 258 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.7757 (p90) REVERT: C 122 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7882 (m-30) REVERT: C 258 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7775 (p90) REVERT: B 258 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.7769 (p90) REVERT: A 122 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.7928 (m-30) REVERT: A 148 TYR cc_start: 0.8524 (m-80) cc_final: 0.8161 (m-80) REVERT: A 255 ARG cc_start: 0.8044 (mmp80) cc_final: 0.7833 (mmp80) outliers start: 26 outliers final: 17 residues processed: 164 average time/residue: 0.1371 time to fit residues: 31.6407 Evaluate side-chains 169 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 13 ASP Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 167 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 24 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 169 HIS C 169 HIS C 233 GLN B 169 HIS A 169 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.145375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.116231 restraints weight = 13633.899| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.95 r_work: 0.2947 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 12865 Z= 0.288 Angle : 0.671 6.481 17535 Z= 0.352 Chirality : 0.050 0.176 1950 Planarity : 0.005 0.028 2235 Dihedral : 5.325 20.238 1685 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.98 % Allowed : 13.09 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.51 (0.21), residues: 1525 helix: 1.30 (0.22), residues: 505 sheet: -0.15 (0.22), residues: 485 loop : -2.11 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 105 TYR 0.015 0.002 TYR C 270 PHE 0.015 0.002 PHE E 308 TRP 0.015 0.002 TRP E 161 HIS 0.005 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00702 (12865) covalent geometry : angle 0.67056 (17535) hydrogen bonds : bond 0.04880 ( 540) hydrogen bonds : angle 4.72438 ( 1575) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 0.546 Fit side-chains REVERT: E 149 THR cc_start: 0.8159 (t) cc_final: 0.7651 (p) REVERT: E 255 ARG cc_start: 0.8033 (mmp80) cc_final: 0.7825 (mmp80) REVERT: E 258 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7437 (p90) REVERT: D 258 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.7879 (p90) REVERT: C 255 ARG cc_start: 0.8121 (mmp80) cc_final: 0.6999 (mmt90) REVERT: C 258 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.7761 (p90) REVERT: B 258 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.7792 (p90) REVERT: A 148 TYR cc_start: 0.8516 (m-80) cc_final: 0.8237 (m-80) outliers start: 41 outliers final: 28 residues processed: 162 average time/residue: 0.1339 time to fit residues: 30.6019 Evaluate side-chains 162 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 167 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 78 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 169 HIS C 169 HIS B 169 HIS A 169 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.152004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.123941 restraints weight = 13233.215| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.57 r_work: 0.3083 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12865 Z= 0.123 Angle : 0.503 6.398 17535 Z= 0.266 Chirality : 0.045 0.169 1950 Planarity : 0.003 0.026 2235 Dihedral : 4.642 15.729 1685 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.04 % Allowed : 13.53 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.21), residues: 1525 helix: 1.84 (0.23), residues: 505 sheet: -0.05 (0.23), residues: 485 loop : -1.99 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 286 TYR 0.010 0.001 TYR B 270 PHE 0.010 0.001 PHE C 236 TRP 0.014 0.001 TRP E 161 HIS 0.003 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00285 (12865) covalent geometry : angle 0.50333 (17535) hydrogen bonds : bond 0.03502 ( 540) hydrogen bonds : angle 4.40689 ( 1575) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.337 Fit side-chains REVERT: E 149 THR cc_start: 0.8090 (t) cc_final: 0.7628 (p) REVERT: E 255 ARG cc_start: 0.7896 (mmp80) cc_final: 0.7612 (mmp80) REVERT: E 258 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.7403 (p90) REVERT: D 93 MET cc_start: 0.8202 (ttm) cc_final: 0.7964 (mmm) REVERT: D 122 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7967 (m-30) REVERT: D 258 TYR cc_start: 0.8316 (OUTLIER) cc_final: 0.7654 (p90) REVERT: C 255 ARG cc_start: 0.7993 (mmp80) cc_final: 0.6810 (mmt90) REVERT: C 258 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.7731 (p90) REVERT: B 258 TYR cc_start: 0.8352 (OUTLIER) cc_final: 0.7761 (p90) REVERT: A 122 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7833 (m-30) REVERT: A 255 ARG cc_start: 0.7948 (mmp80) cc_final: 0.6784 (mmt90) outliers start: 28 outliers final: 20 residues processed: 175 average time/residue: 0.1387 time to fit residues: 33.5078 Evaluate side-chains 174 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 167 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 119 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 117 optimal weight: 0.0170 chunk 132 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.7224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 285 HIS D 169 HIS C 169 HIS C 285 HIS B 169 HIS A 169 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.154267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.127853 restraints weight = 13235.594| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.41 r_work: 0.3115 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12865 Z= 0.098 Angle : 0.467 6.258 17535 Z= 0.245 Chirality : 0.044 0.220 1950 Planarity : 0.003 0.030 2235 Dihedral : 4.245 15.344 1685 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.75 % Allowed : 13.89 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.15 (0.22), residues: 1525 helix: 2.08 (0.23), residues: 505 sheet: -0.07 (0.24), residues: 470 loop : -1.64 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 286 TYR 0.008 0.001 TYR C 38 PHE 0.012 0.001 PHE C 282 TRP 0.012 0.001 TRP E 161 HIS 0.003 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00221 (12865) covalent geometry : angle 0.46664 (17535) hydrogen bonds : bond 0.03025 ( 540) hydrogen bonds : angle 4.23054 ( 1575) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.516 Fit side-chains REVERT: E 114 MET cc_start: 0.8469 (mtm) cc_final: 0.8224 (mtp) REVERT: E 255 ARG cc_start: 0.7809 (mmp80) cc_final: 0.6912 (mmt90) REVERT: E 258 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.7417 (p90) REVERT: D 122 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7944 (m-30) REVERT: D 258 TYR cc_start: 0.8226 (OUTLIER) cc_final: 0.7536 (p90) REVERT: C 258 TYR cc_start: 0.8256 (OUTLIER) cc_final: 0.7490 (p90) REVERT: B 34 LYS cc_start: 0.8693 (mttp) cc_final: 0.8478 (mttt) REVERT: B 258 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7804 (p90) REVERT: A 122 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7853 (m-30) outliers start: 24 outliers final: 14 residues processed: 179 average time/residue: 0.1246 time to fit residues: 31.8607 Evaluate side-chains 173 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 167 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 106 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 148 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 233 GLN A 169 HIS A 233 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.147507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.122063 restraints weight = 13437.014| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.16 r_work: 0.3013 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 12865 Z= 0.258 Angle : 0.636 6.183 17535 Z= 0.333 Chirality : 0.049 0.206 1950 Planarity : 0.005 0.032 2235 Dihedral : 5.109 18.590 1685 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.89 % Allowed : 13.96 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.35 (0.21), residues: 1525 helix: 1.55 (0.23), residues: 505 sheet: -0.20 (0.23), residues: 485 loop : -2.02 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 255 TYR 0.012 0.002 TYR B 270 PHE 0.020 0.002 PHE D 236 TRP 0.013 0.002 TRP E 161 HIS 0.005 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00626 (12865) covalent geometry : angle 0.63567 (17535) hydrogen bonds : bond 0.04679 ( 540) hydrogen bonds : angle 4.62545 ( 1575) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.395 Fit side-chains REVERT: E 149 THR cc_start: 0.8188 (t) cc_final: 0.7773 (p) REVERT: E 258 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.7459 (p90) REVERT: D 258 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.7904 (p90) REVERT: C 149 THR cc_start: 0.8230 (t) cc_final: 0.7748 (p) REVERT: C 255 ARG cc_start: 0.8105 (mmp80) cc_final: 0.7097 (mmt90) REVERT: C 258 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.7829 (p90) REVERT: B 255 ARG cc_start: 0.8256 (mmp80) cc_final: 0.7092 (mmt90) REVERT: B 258 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.7861 (p90) REVERT: A 148 TYR cc_start: 0.8554 (m-80) cc_final: 0.8257 (m-80) outliers start: 26 outliers final: 20 residues processed: 152 average time/residue: 0.1183 time to fit residues: 25.7667 Evaluate side-chains 153 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 167 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 61 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 84 optimal weight: 0.0050 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 169 HIS C 169 HIS A 169 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.150813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.121684 restraints weight = 13287.493| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.49 r_work: 0.3096 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12865 Z= 0.131 Angle : 0.505 6.272 17535 Z= 0.266 Chirality : 0.045 0.207 1950 Planarity : 0.004 0.027 2235 Dihedral : 4.585 15.917 1685 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.89 % Allowed : 14.18 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.07 (0.22), residues: 1525 helix: 1.90 (0.23), residues: 505 sheet: -0.08 (0.23), residues: 485 loop : -1.93 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 255 TYR 0.011 0.001 TYR E 148 PHE 0.014 0.001 PHE D 236 TRP 0.014 0.001 TRP E 161 HIS 0.003 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00307 (12865) covalent geometry : angle 0.50498 (17535) hydrogen bonds : bond 0.03553 ( 540) hydrogen bonds : angle 4.40840 ( 1575) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2845.28 seconds wall clock time: 49 minutes 34.19 seconds (2974.19 seconds total)