Starting phenix.real_space_refine on Wed Mar 4 01:29:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kh0_22872/03_2026/7kh0_22872.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kh0_22872/03_2026/7kh0_22872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kh0_22872/03_2026/7kh0_22872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kh0_22872/03_2026/7kh0_22872.map" model { file = "/net/cci-nas-00/data/ceres_data/7kh0_22872/03_2026/7kh0_22872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kh0_22872/03_2026/7kh0_22872.cif" } resolution = 2.8 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= 0.051 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 68 5.16 5 C 6270 2.51 5 N 1728 2.21 5 O 1832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9898 Number of models: 1 Model: "" Number of chains: 8 Chain: "R" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2117 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 259} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "A" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1869 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 462 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 4, 'TRANS': 55} Chain: "S" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1807 Classifications: {'peptide': 236} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Time building chain proxies: 2.42, per 1000 atoms: 0.24 Number of scatterers: 9898 At special positions: 0 Unit cell: (83.3, 126.65, 133.45, 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 68 16.00 O 1832 8.00 N 1728 7.00 C 6270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 112 " - pdb=" SG CYS R 192 " distance=2.03 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 6 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 399.8 milliseconds 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2374 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 34.6% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'R' and resid 33 through 68 Processing helix chain 'R' and resid 72 through 103 removed outlier: 3.998A pdb=" N LEU R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Proline residue: R 95 - end of helix Processing helix chain 'R' and resid 108 through 143 removed outlier: 3.772A pdb=" N CYS R 112 " --> pdb=" O PRO R 108 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG R 113 " --> pdb=" O ASP R 109 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLY R 122 " --> pdb=" O LEU R 118 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N MET R 123 " --> pdb=" O GLN R 119 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER R 127 " --> pdb=" O MET R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 171 Processing helix chain 'R' and resid 172 through 178 removed outlier: 4.418A pdb=" N PHE R 176 " --> pdb=" O LEU R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 237 removed outlier: 3.583A pdb=" N TYR R 205 " --> pdb=" O GLY R 201 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL R 206 " --> pdb=" O ARG R 202 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR R 207 " --> pdb=" O ARG R 203 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ALA R 216 " --> pdb=" O MET R 212 " (cutoff:3.500A) Proline residue: R 217 - end of helix removed outlier: 3.779A pdb=" N VAL R 237 " --> pdb=" O HIS R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 265 through 297 removed outlier: 3.624A pdb=" N VAL R 275 " --> pdb=" O ARG R 271 " (cutoff:3.500A) Proline residue: R 286 - end of helix Processing helix chain 'R' and resid 304 through 311 removed outlier: 3.554A pdb=" N VAL R 308 " --> pdb=" O GLY R 304 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU R 309 " --> pdb=" O ALA R 305 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU R 310 " --> pdb=" O PRO R 306 " (cutoff:3.500A) Processing helix chain 'R' and resid 315 through 319 Processing helix chain 'R' and resid 320 through 328 Processing helix chain 'R' and resid 330 through 339 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'A' and resid 13 through 38 removed outlier: 3.715A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.553A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.800A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.869A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.675A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.928A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.662A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.746A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.574A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.708A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.800A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.782A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.758A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.940A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.632A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.746A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.280A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.501A pdb=" N THR S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.541A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 141 removed outlier: 3.588A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 149 removed outlier: 6.711A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.644A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1293 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: 1.55 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2276 1.33 - 1.45: 2354 1.45 - 1.58: 5380 1.58 - 1.70: 0 1.70 - 1.83: 97 Bond restraints: 10107 Sorted by residual: bond pdb=" N GLU R 231 " pdb=" CA GLU R 231 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.28e-02 6.10e+03 1.15e+01 bond pdb=" N LEU R 172 " pdb=" CA LEU R 172 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.04e-02 9.25e+03 9.24e+00 bond pdb=" N CYS R 195 " pdb=" CA CYS R 195 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.23e-02 6.61e+03 8.48e+00 bond pdb=" N TRP R 164 " pdb=" CA TRP R 164 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.21e-02 6.83e+03 8.43e+00 bond pdb=" N TRP R 293 " pdb=" CA TRP R 293 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.21e-02 6.83e+03 7.63e+00 ... (remaining 10102 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 13474 2.60 - 5.19: 201 5.19 - 7.79: 22 7.79 - 10.38: 5 10.38 - 12.98: 1 Bond angle restraints: 13703 Sorted by residual: angle pdb=" N GLU R 303 " pdb=" CA GLU R 303 " pdb=" C GLU R 303 " ideal model delta sigma weight residual 112.88 99.90 12.98 1.29e+00 6.01e-01 1.01e+02 angle pdb=" C LEU A 388 " pdb=" N ARG A 389 " pdb=" CA ARG A 389 " ideal model delta sigma weight residual 121.66 111.68 9.98 1.76e+00 3.23e-01 3.22e+01 angle pdb=" C PHE R 178 " pdb=" CA PHE R 178 " pdb=" CB PHE R 178 " ideal model delta sigma weight residual 111.41 120.44 -9.03 1.65e+00 3.67e-01 3.00e+01 angle pdb=" N TYR L 2 " pdb=" CA TYR L 2 " pdb=" C TYR L 2 " ideal model delta sigma weight residual 112.90 105.83 7.07 1.31e+00 5.83e-01 2.92e+01 angle pdb=" O ILE A 383 " pdb=" C ILE A 383 " pdb=" N GLN A 384 " ideal model delta sigma weight residual 121.80 116.00 5.80 1.13e+00 7.83e-01 2.64e+01 ... (remaining 13698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 5491 17.77 - 35.54: 425 35.54 - 53.31: 73 53.31 - 71.08: 12 71.08 - 88.85: 13 Dihedral angle restraints: 6014 sinusoidal: 2336 harmonic: 3678 Sorted by residual: dihedral pdb=" CB CYS R 112 " pdb=" SG CYS R 112 " pdb=" SG CYS R 192 " pdb=" CB CYS R 192 " ideal model delta sinusoidal sigma weight residual -86.00 -150.93 64.93 1 1.00e+01 1.00e-02 5.53e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -21.13 -64.87 1 1.00e+01 1.00e-02 5.52e+01 dihedral pdb=" CB CYS L 1 " pdb=" SG CYS L 1 " pdb=" SG CYS L 6 " pdb=" CB CYS L 6 " ideal model delta sinusoidal sigma weight residual 93.00 50.36 42.64 1 1.00e+01 1.00e-02 2.54e+01 ... (remaining 6011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1289 0.066 - 0.131: 225 0.131 - 0.196: 17 0.196 - 0.262: 6 0.262 - 0.327: 2 Chirality restraints: 1539 Sorted by residual: chirality pdb=" CA CYS L 1 " pdb=" N CYS L 1 " pdb=" C CYS L 1 " pdb=" CB CYS L 1 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA PHE R 178 " pdb=" N PHE R 178 " pdb=" C PHE R 178 " pdb=" CB PHE R 178 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA ARG R 181 " pdb=" N ARG R 181 " pdb=" C ARG R 181 " pdb=" CB ARG R 181 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1536 not shown) Planarity restraints: 1748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 383 " 0.016 2.00e-02 2.50e+03 3.07e-02 9.43e+00 pdb=" C ILE A 383 " -0.053 2.00e-02 2.50e+03 pdb=" O ILE A 383 " 0.019 2.00e-02 2.50e+03 pdb=" N GLN A 384 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 178 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.34e+00 pdb=" C PHE R 178 " -0.040 2.00e-02 2.50e+03 pdb=" O PHE R 178 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA R 179 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN R 291 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.12e+00 pdb=" C GLN R 291 " -0.035 2.00e-02 2.50e+03 pdb=" O GLN R 291 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU R 292 " 0.012 2.00e-02 2.50e+03 ... (remaining 1745 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 425 2.72 - 3.26: 9570 3.26 - 3.81: 15477 3.81 - 4.35: 18884 4.35 - 4.90: 33693 Nonbonded interactions: 78049 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.171 3.040 nonbonded pdb=" NH2 ARG B 8 " pdb=" OE1 GLN N 120 " model vdw 2.177 3.120 nonbonded pdb=" NH2 ARG S 202 " pdb=" OE2 GLU S 220 " model vdw 2.196 3.120 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.217 3.040 nonbonded pdb=" OE2 GLU A 344 " pdb=" NH1 ARG A 347 " model vdw 2.239 3.120 ... (remaining 78044 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 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: 1.120 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.160 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 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 0.096 10114 Z= 0.299 Angle : 0.759 12.977 13715 Z= 0.477 Chirality : 0.050 0.327 1539 Planarity : 0.004 0.049 1748 Dihedral : 13.348 88.851 3622 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.57 % Allowed : 0.85 % Favored : 98.59 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 2.13 % 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 are not related in a simple way. whole: 0.17 (0.23), residues: 1245 helix: 1.42 (0.27), residues: 380 sheet: 0.24 (0.28), residues: 338 loop : -0.91 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 8 TYR 0.016 0.001 TYR S 190 PHE 0.018 0.001 PHE R 77 TRP 0.011 0.001 TRP B 332 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00493 (10107) covalent geometry : angle 0.75839 (13703) SS BOND : bond 0.00357 ( 6) SS BOND : angle 1.24267 ( 12) hydrogen bonds : bond 0.18098 ( 459) hydrogen bonds : angle 6.74023 ( 1293) Misc. bond : bond 0.09611 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 194 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: R 85 ASP cc_start: 0.8250 (t70) cc_final: 0.7964 (t70) REVERT: R 136 ASP cc_start: 0.8720 (t0) cc_final: 0.8470 (t0) REVERT: R 323 TRP cc_start: 0.7914 (m100) cc_final: 0.7620 (m-10) REVERT: B 8 ARG cc_start: 0.8565 (mtt180) cc_final: 0.7986 (mmt180) REVERT: B 10 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8723 (mm-30) REVERT: B 312 ASP cc_start: 0.8287 (t0) cc_final: 0.8060 (t0) REVERT: L 7 PRO cc_start: 0.8921 (Cg_exo) cc_final: 0.8700 (Cg_endo) REVERT: S 73 ASP cc_start: 0.8577 (t70) cc_final: 0.7979 (t0) REVERT: S 244 LYS cc_start: 0.8716 (tttt) cc_final: 0.8293 (ttpt) REVERT: S 246 GLU cc_start: 0.7611 (mp0) cc_final: 0.7067 (mp0) REVERT: N 73 ASP cc_start: 0.8589 (t70) cc_final: 0.7984 (t0) outliers start: 6 outliers final: 0 residues processed: 198 average time/residue: 0.7008 time to fit residues: 146.6677 Evaluate side-chains 141 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 0.0570 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 174 GLN ** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN A 294 GLN ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.081585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.055214 restraints weight = 22497.532| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 3.29 r_work: 0.2591 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10114 Z= 0.149 Angle : 0.596 7.367 13715 Z= 0.312 Chirality : 0.044 0.176 1539 Planarity : 0.004 0.044 1748 Dihedral : 4.384 36.100 1387 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.41 % Allowed : 10.93 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 are not related in a simple way. whole: 0.44 (0.23), residues: 1245 helix: 1.68 (0.26), residues: 386 sheet: 0.54 (0.28), residues: 337 loop : -0.92 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 356 TYR 0.025 0.001 TYR S 190 PHE 0.012 0.001 PHE S 203 TRP 0.022 0.001 TRP R 193 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00336 (10107) covalent geometry : angle 0.59480 (13703) SS BOND : bond 0.00420 ( 6) SS BOND : angle 1.31391 ( 12) hydrogen bonds : bond 0.04813 ( 459) hydrogen bonds : angle 4.77086 ( 1293) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 136 ASP cc_start: 0.8767 (t0) cc_final: 0.8507 (t0) REVERT: B 10 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8739 (mm-30) REVERT: B 15 LYS cc_start: 0.8911 (mmmm) cc_final: 0.8597 (tptt) REVERT: B 312 ASP cc_start: 0.9030 (t0) cc_final: 0.8657 (t0) REVERT: G 20 LYS cc_start: 0.9066 (tppp) cc_final: 0.8559 (mtmp) REVERT: G 21 MET cc_start: 0.9025 (tpp) cc_final: 0.8637 (ttt) REVERT: G 22 GLU cc_start: 0.8866 (tt0) cc_final: 0.8553 (tt0) REVERT: G 58 GLU cc_start: 0.8579 (pm20) cc_final: 0.8325 (pm20) REVERT: S 73 ASP cc_start: 0.8460 (t70) cc_final: 0.7716 (t0) REVERT: S 76 LYS cc_start: 0.9135 (ptpp) cc_final: 0.8843 (ptpp) REVERT: N 39 GLN cc_start: 0.9169 (tm-30) cc_final: 0.8875 (tp40) REVERT: N 73 ASP cc_start: 0.7697 (t70) cc_final: 0.7031 (t0) REVERT: N 83 MET cc_start: 0.9344 (OUTLIER) cc_final: 0.8803 (mtp) outliers start: 15 outliers final: 7 residues processed: 167 average time/residue: 0.6711 time to fit residues: 118.9639 Evaluate side-chains 151 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 74 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 56 optimal weight: 0.0050 chunk 67 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 overall best weight: 1.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 92 GLN ** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN G 24 ASN S 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.081232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.054923 restraints weight = 22780.271| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 3.27 r_work: 0.2585 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10114 Z= 0.154 Angle : 0.569 7.338 13715 Z= 0.296 Chirality : 0.043 0.155 1539 Planarity : 0.004 0.043 1748 Dihedral : 4.253 33.093 1387 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.60 % Allowed : 13.01 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 are not related in a simple way. whole: 0.62 (0.23), residues: 1245 helix: 1.86 (0.26), residues: 386 sheet: 0.69 (0.28), residues: 335 loop : -0.87 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 105 TYR 0.019 0.001 TYR S 190 PHE 0.014 0.001 PHE S 203 TRP 0.019 0.001 TRP R 193 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00359 (10107) covalent geometry : angle 0.56844 (13703) SS BOND : bond 0.00442 ( 6) SS BOND : angle 1.23334 ( 12) hydrogen bonds : bond 0.04427 ( 459) hydrogen bonds : angle 4.42390 ( 1293) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 85 ASP cc_start: 0.7990 (t70) cc_final: 0.7703 (t70) REVERT: R 136 ASP cc_start: 0.8824 (t0) cc_final: 0.8579 (t0) REVERT: B 10 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8739 (mm-30) REVERT: B 15 LYS cc_start: 0.8913 (mmmm) cc_final: 0.8633 (tptt) REVERT: B 59 TYR cc_start: 0.9316 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: B 217 MET cc_start: 0.8311 (ptm) cc_final: 0.7797 (ppp) REVERT: B 312 ASP cc_start: 0.9021 (t0) cc_final: 0.8645 (t0) REVERT: G 14 LYS cc_start: 0.9175 (mmmm) cc_final: 0.8839 (mmpt) REVERT: G 20 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8549 (mtmp) REVERT: G 21 MET cc_start: 0.9033 (tpp) cc_final: 0.8689 (ttt) REVERT: G 22 GLU cc_start: 0.8904 (tt0) cc_final: 0.8671 (tt0) REVERT: G 58 GLU cc_start: 0.8582 (pm20) cc_final: 0.8291 (pm20) REVERT: S 43 LYS cc_start: 0.9169 (mmtm) cc_final: 0.8946 (mmpt) REVERT: S 73 ASP cc_start: 0.8529 (t70) cc_final: 0.7638 (t0) REVERT: S 76 LYS cc_start: 0.9093 (ptpp) cc_final: 0.8725 (ptpp) REVERT: N 39 GLN cc_start: 0.9198 (tm-30) cc_final: 0.8811 (tp40) REVERT: N 73 ASP cc_start: 0.7779 (t70) cc_final: 0.7060 (t0) REVERT: N 83 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.8832 (mtp) outliers start: 17 outliers final: 8 residues processed: 162 average time/residue: 0.6688 time to fit residues: 115.1721 Evaluate side-chains 157 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 80 HIS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 39 optimal weight: 0.7980 chunk 115 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 0.0050 chunk 18 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.083479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.057282 restraints weight = 22598.452| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 3.29 r_work: 0.2640 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10114 Z= 0.103 Angle : 0.531 7.809 13715 Z= 0.272 Chirality : 0.041 0.135 1539 Planarity : 0.004 0.042 1748 Dihedral : 3.947 25.828 1387 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.60 % Allowed : 15.08 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 are not related in a simple way. whole: 0.77 (0.23), residues: 1245 helix: 2.03 (0.26), residues: 386 sheet: 0.82 (0.28), residues: 325 loop : -0.84 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 13 TYR 0.018 0.001 TYR S 190 PHE 0.011 0.001 PHE A 212 TRP 0.018 0.001 TRP R 193 HIS 0.004 0.000 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00230 (10107) covalent geometry : angle 0.53070 (13703) SS BOND : bond 0.00337 ( 6) SS BOND : angle 0.93410 ( 12) hydrogen bonds : bond 0.03641 ( 459) hydrogen bonds : angle 4.10152 ( 1293) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 85 ASP cc_start: 0.7889 (t70) cc_final: 0.7585 (t70) REVERT: R 100 LYS cc_start: 0.8796 (mmtm) cc_final: 0.8268 (mttm) REVERT: B 10 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8718 (mm-30) REVERT: B 15 LYS cc_start: 0.8919 (mmmm) cc_final: 0.8663 (tptt) REVERT: B 59 TYR cc_start: 0.9294 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: B 214 ARG cc_start: 0.9055 (mmm-85) cc_final: 0.8784 (mmm-85) REVERT: B 217 MET cc_start: 0.8346 (ptm) cc_final: 0.7816 (ppp) REVERT: B 312 ASP cc_start: 0.9025 (t0) cc_final: 0.8649 (t0) REVERT: A 296 LEU cc_start: 0.9028 (mm) cc_final: 0.8568 (tt) REVERT: A 317 ARG cc_start: 0.8869 (mtm110) cc_final: 0.8577 (mtm110) REVERT: G 14 LYS cc_start: 0.9144 (mmmm) cc_final: 0.8808 (mmpt) REVERT: G 20 LYS cc_start: 0.9010 (tppp) cc_final: 0.8615 (mtmp) REVERT: G 21 MET cc_start: 0.9057 (tpp) cc_final: 0.8697 (ttt) REVERT: G 22 GLU cc_start: 0.8869 (tt0) cc_final: 0.8571 (tt0) REVERT: G 58 GLU cc_start: 0.8478 (pm20) cc_final: 0.8270 (pm20) REVERT: S 73 ASP cc_start: 0.8492 (t70) cc_final: 0.7651 (t0) REVERT: S 76 LYS cc_start: 0.9055 (ptpp) cc_final: 0.8699 (ptpp) REVERT: N 39 GLN cc_start: 0.9175 (tm-30) cc_final: 0.8741 (tp40) REVERT: N 73 ASP cc_start: 0.7702 (t70) cc_final: 0.7055 (t0) REVERT: N 83 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8772 (mtp) REVERT: N 105 ARG cc_start: 0.8462 (ptm160) cc_final: 0.8222 (ttp-110) outliers start: 17 outliers final: 6 residues processed: 169 average time/residue: 0.6628 time to fit residues: 119.1128 Evaluate side-chains 153 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 96 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.081308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.054706 restraints weight = 22819.407| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.34 r_work: 0.2585 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10114 Z= 0.156 Angle : 0.562 8.147 13715 Z= 0.290 Chirality : 0.042 0.156 1539 Planarity : 0.004 0.042 1748 Dihedral : 3.966 25.167 1387 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.36 % Allowed : 15.36 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 are not related in a simple way. whole: 0.80 (0.23), residues: 1245 helix: 2.03 (0.26), residues: 392 sheet: 0.82 (0.28), residues: 326 loop : -0.83 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 13 TYR 0.017 0.001 TYR S 190 PHE 0.010 0.001 PHE S 203 TRP 0.019 0.001 TRP R 193 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00366 (10107) covalent geometry : angle 0.56127 (13703) SS BOND : bond 0.00481 ( 6) SS BOND : angle 1.12012 ( 12) hydrogen bonds : bond 0.04127 ( 459) hydrogen bonds : angle 4.14907 ( 1293) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: R 85 ASP cc_start: 0.7990 (t70) cc_final: 0.7698 (t70) REVERT: B 10 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8762 (mm-30) REVERT: B 15 LYS cc_start: 0.8911 (mmmm) cc_final: 0.8677 (tptt) REVERT: B 59 TYR cc_start: 0.9327 (OUTLIER) cc_final: 0.8029 (m-80) REVERT: B 217 MET cc_start: 0.8438 (ptm) cc_final: 0.7845 (ppp) REVERT: B 312 ASP cc_start: 0.9028 (t0) cc_final: 0.8620 (t0) REVERT: A 296 LEU cc_start: 0.9018 (mm) cc_final: 0.8580 (tt) REVERT: A 317 ARG cc_start: 0.8842 (mtm110) cc_final: 0.8546 (mtm180) REVERT: A 392 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8624 (mt-10) REVERT: G 14 LYS cc_start: 0.9141 (mmmm) cc_final: 0.8794 (mmpt) REVERT: G 20 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8672 (mtmp) REVERT: G 21 MET cc_start: 0.9073 (tpp) cc_final: 0.8637 (ttt) REVERT: G 22 GLU cc_start: 0.8893 (tt0) cc_final: 0.8666 (tt0) REVERT: G 58 GLU cc_start: 0.8589 (pm20) cc_final: 0.8359 (pm20) REVERT: S 43 LYS cc_start: 0.9100 (mmtm) cc_final: 0.8880 (mmpt) REVERT: S 73 ASP cc_start: 0.8438 (t70) cc_final: 0.7685 (t0) REVERT: S 216 ILE cc_start: 0.8806 (mm) cc_final: 0.8605 (mm) REVERT: N 46 GLU cc_start: 0.8567 (pt0) cc_final: 0.8299 (pt0) REVERT: N 73 ASP cc_start: 0.7630 (t70) cc_final: 0.6955 (t0) REVERT: N 83 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8734 (mtp) outliers start: 25 outliers final: 9 residues processed: 166 average time/residue: 0.6612 time to fit residues: 116.6861 Evaluate side-chains 160 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 98 optimal weight: 0.4980 chunk 117 optimal weight: 3.9990 chunk 53 optimal weight: 0.1980 chunk 74 optimal weight: 0.0010 chunk 43 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN G 24 ASN S 13 GLN S 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.084023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.057572 restraints weight = 22632.991| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 3.32 r_work: 0.2650 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10114 Z= 0.104 Angle : 0.550 8.975 13715 Z= 0.279 Chirality : 0.041 0.240 1539 Planarity : 0.004 0.046 1748 Dihedral : 3.759 20.554 1387 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.89 % Allowed : 16.21 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 are not related in a simple way. whole: 0.95 (0.23), residues: 1245 helix: 2.12 (0.26), residues: 393 sheet: 0.95 (0.28), residues: 332 loop : -0.76 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 105 TYR 0.018 0.001 TYR S 190 PHE 0.013 0.001 PHE A 212 TRP 0.023 0.001 TRP R 323 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00234 (10107) covalent geometry : angle 0.54932 (13703) SS BOND : bond 0.00364 ( 6) SS BOND : angle 0.84313 ( 12) hydrogen bonds : bond 0.03390 ( 459) hydrogen bonds : angle 3.94659 ( 1293) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: R 85 ASP cc_start: 0.7853 (t70) cc_final: 0.7557 (t70) REVERT: R 100 LYS cc_start: 0.8698 (tppt) cc_final: 0.8147 (ttmp) REVERT: R 311 MET cc_start: 0.8656 (mtp) cc_final: 0.8338 (ttm) REVERT: R 323 TRP cc_start: 0.8052 (m100) cc_final: 0.7643 (m-10) REVERT: B 10 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8724 (mm-30) REVERT: B 15 LYS cc_start: 0.8926 (mmmm) cc_final: 0.8695 (tptt) REVERT: B 217 MET cc_start: 0.8478 (ptm) cc_final: 0.7885 (ppp) REVERT: B 312 ASP cc_start: 0.9035 (t0) cc_final: 0.8646 (t0) REVERT: A 296 LEU cc_start: 0.9035 (mm) cc_final: 0.8614 (tt) REVERT: A 392 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8643 (mt-10) REVERT: G 13 ARG cc_start: 0.8849 (ttm110) cc_final: 0.8499 (ttm110) REVERT: G 14 LYS cc_start: 0.9140 (mmmm) cc_final: 0.8784 (mmpt) REVERT: G 17 GLU cc_start: 0.9314 (tp30) cc_final: 0.8995 (mm-30) REVERT: G 18 GLN cc_start: 0.8442 (tp40) cc_final: 0.8167 (tp-100) REVERT: G 20 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8755 (mtmm) REVERT: G 21 MET cc_start: 0.9079 (tpp) cc_final: 0.8670 (ttt) REVERT: G 22 GLU cc_start: 0.8862 (tt0) cc_final: 0.8608 (tt0) REVERT: G 58 GLU cc_start: 0.8527 (pm20) cc_final: 0.8307 (pm20) REVERT: S 43 LYS cc_start: 0.9116 (mmtm) cc_final: 0.8877 (mmpt) REVERT: S 73 ASP cc_start: 0.8441 (t70) cc_final: 0.7670 (t0) REVERT: S 234 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8585 (pt0) REVERT: N 5 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8378 (tp40) REVERT: N 46 GLU cc_start: 0.8378 (pt0) cc_final: 0.8147 (pt0) REVERT: N 73 ASP cc_start: 0.7611 (t70) cc_final: 0.7012 (t0) REVERT: N 83 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8742 (mtp) outliers start: 20 outliers final: 6 residues processed: 168 average time/residue: 0.6927 time to fit residues: 123.5738 Evaluate side-chains 158 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 52 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 92 GLN R 119 GLN B 88 ASN G 24 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.081461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.055013 restraints weight = 22593.872| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.30 r_work: 0.2586 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10114 Z= 0.155 Angle : 0.582 8.796 13715 Z= 0.299 Chirality : 0.043 0.206 1539 Planarity : 0.004 0.046 1748 Dihedral : 3.896 22.819 1387 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.60 % Allowed : 17.91 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 are not related in a simple way. whole: 0.94 (0.23), residues: 1245 helix: 2.13 (0.26), residues: 392 sheet: 0.91 (0.28), residues: 325 loop : -0.73 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 105 TYR 0.017 0.001 TYR S 190 PHE 0.012 0.001 PHE S 203 TRP 0.017 0.001 TRP R 193 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00365 (10107) covalent geometry : angle 0.58150 (13703) SS BOND : bond 0.00445 ( 6) SS BOND : angle 0.94113 ( 12) hydrogen bonds : bond 0.04065 ( 459) hydrogen bonds : angle 4.06642 ( 1293) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: R 85 ASP cc_start: 0.7968 (t70) cc_final: 0.7691 (t70) REVERT: R 100 LYS cc_start: 0.8696 (tppt) cc_final: 0.8139 (mttm) REVERT: R 311 MET cc_start: 0.8704 (mtp) cc_final: 0.8395 (ttm) REVERT: R 323 TRP cc_start: 0.8106 (m100) cc_final: 0.7731 (m-10) REVERT: B 10 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8806 (mm-30) REVERT: B 15 LYS cc_start: 0.8925 (mmmm) cc_final: 0.8691 (tptt) REVERT: B 59 TYR cc_start: 0.9231 (OUTLIER) cc_final: 0.8097 (m-80) REVERT: B 217 MET cc_start: 0.8555 (ptm) cc_final: 0.7960 (ppp) REVERT: B 312 ASP cc_start: 0.9044 (t0) cc_final: 0.8630 (t0) REVERT: A 296 LEU cc_start: 0.9043 (mm) cc_final: 0.8642 (tt) REVERT: A 317 ARG cc_start: 0.8765 (mtm110) cc_final: 0.8493 (mtm110) REVERT: A 392 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8657 (mt-10) REVERT: G 14 LYS cc_start: 0.9144 (mmmm) cc_final: 0.8815 (mmpt) REVERT: G 20 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8774 (mtmp) REVERT: G 21 MET cc_start: 0.9070 (tpp) cc_final: 0.8594 (ttt) REVERT: G 22 GLU cc_start: 0.8886 (tt0) cc_final: 0.8684 (tt0) REVERT: G 58 GLU cc_start: 0.8612 (pm20) cc_final: 0.8373 (pm20) REVERT: S 43 LYS cc_start: 0.9049 (mmtm) cc_final: 0.8802 (mmpt) REVERT: S 73 ASP cc_start: 0.8439 (t70) cc_final: 0.7614 (t0) REVERT: S 186 GLN cc_start: 0.8789 (tt0) cc_final: 0.8525 (pt0) REVERT: S 234 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8647 (pt0) REVERT: N 5 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8409 (tp40) REVERT: N 73 ASP cc_start: 0.7688 (t70) cc_final: 0.7008 (t0) REVERT: N 83 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8741 (mtp) outliers start: 17 outliers final: 7 residues processed: 161 average time/residue: 0.6511 time to fit residues: 111.3114 Evaluate side-chains 160 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 113 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 ASN S 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.082210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.055786 restraints weight = 22509.098| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.30 r_work: 0.2607 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10114 Z= 0.131 Angle : 0.587 8.372 13715 Z= 0.299 Chirality : 0.042 0.190 1539 Planarity : 0.004 0.053 1748 Dihedral : 3.861 21.898 1387 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.60 % Allowed : 18.47 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 are not related in a simple way. whole: 0.95 (0.23), residues: 1245 helix: 2.07 (0.26), residues: 393 sheet: 0.93 (0.28), residues: 325 loop : -0.69 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 105 TYR 0.017 0.001 TYR S 190 PHE 0.011 0.001 PHE A 212 TRP 0.019 0.001 TRP R 193 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00306 (10107) covalent geometry : angle 0.58713 (13703) SS BOND : bond 0.00411 ( 6) SS BOND : angle 0.88333 ( 12) hydrogen bonds : bond 0.03793 ( 459) hydrogen bonds : angle 3.99923 ( 1293) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: R 85 ASP cc_start: 0.7959 (t70) cc_final: 0.7676 (t70) REVERT: R 100 LYS cc_start: 0.8691 (tppt) cc_final: 0.8136 (mttm) REVERT: R 311 MET cc_start: 0.8715 (mtp) cc_final: 0.8433 (mtm) REVERT: R 323 TRP cc_start: 0.8145 (m100) cc_final: 0.7751 (m-10) REVERT: B 10 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8839 (mm-30) REVERT: B 15 LYS cc_start: 0.8922 (mmmm) cc_final: 0.8705 (tptt) REVERT: B 25 CYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8014 (t) REVERT: B 59 TYR cc_start: 0.9189 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: B 217 MET cc_start: 0.8637 (ptm) cc_final: 0.8049 (ppp) REVERT: B 254 ASP cc_start: 0.8544 (t0) cc_final: 0.7874 (t0) REVERT: B 312 ASP cc_start: 0.9047 (t0) cc_final: 0.8641 (t0) REVERT: A 296 LEU cc_start: 0.9044 (mm) cc_final: 0.8644 (tt) REVERT: A 317 ARG cc_start: 0.8758 (mtm110) cc_final: 0.8528 (mtm180) REVERT: A 392 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8633 (mt-10) REVERT: G 14 LYS cc_start: 0.9135 (mmmm) cc_final: 0.8805 (mmpt) REVERT: G 17 GLU cc_start: 0.9238 (tp30) cc_final: 0.9032 (mm-30) REVERT: G 21 MET cc_start: 0.9083 (tpp) cc_final: 0.8654 (ttt) REVERT: G 58 GLU cc_start: 0.8598 (pm20) cc_final: 0.8360 (pm20) REVERT: S 73 ASP cc_start: 0.8450 (t70) cc_final: 0.7606 (t0) REVERT: S 76 LYS cc_start: 0.8969 (ptpp) cc_final: 0.8600 (ptpp) REVERT: S 186 GLN cc_start: 0.8777 (tt0) cc_final: 0.8512 (pt0) REVERT: S 234 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8614 (pt0) REVERT: N 5 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8408 (tp40) REVERT: N 83 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8757 (mtp) outliers start: 17 outliers final: 7 residues processed: 162 average time/residue: 0.6286 time to fit residues: 108.2695 Evaluate side-chains 158 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 52 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 13 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.080343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.053947 restraints weight = 22725.493| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 3.29 r_work: 0.2564 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10114 Z= 0.199 Angle : 0.631 10.312 13715 Z= 0.322 Chirality : 0.044 0.176 1539 Planarity : 0.004 0.053 1748 Dihedral : 4.051 23.981 1387 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.70 % Allowed : 18.38 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 are not related in a simple way. whole: 0.84 (0.23), residues: 1245 helix: 1.93 (0.26), residues: 394 sheet: 0.88 (0.28), residues: 325 loop : -0.72 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 105 TYR 0.015 0.001 TYR S 190 PHE 0.011 0.001 PHE S 203 TRP 0.019 0.001 TRP R 193 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00472 (10107) covalent geometry : angle 0.63028 (13703) SS BOND : bond 0.00506 ( 6) SS BOND : angle 1.11318 ( 12) hydrogen bonds : bond 0.04378 ( 459) hydrogen bonds : angle 4.17781 ( 1293) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 85 ASP cc_start: 0.7981 (t70) cc_final: 0.7712 (t70) REVERT: R 100 LYS cc_start: 0.8694 (tppt) cc_final: 0.8137 (mttm) REVERT: R 311 MET cc_start: 0.8720 (mtp) cc_final: 0.8434 (ttm) REVERT: R 323 TRP cc_start: 0.8164 (m100) cc_final: 0.7800 (m-10) REVERT: B 10 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8876 (mm-30) REVERT: B 15 LYS cc_start: 0.8934 (mmmm) cc_final: 0.8719 (tptt) REVERT: B 59 TYR cc_start: 0.9260 (OUTLIER) cc_final: 0.8127 (m-80) REVERT: B 217 MET cc_start: 0.8714 (ptm) cc_final: 0.8135 (ppp) REVERT: B 254 ASP cc_start: 0.8603 (t0) cc_final: 0.7957 (t0) REVERT: B 312 ASP cc_start: 0.9041 (t0) cc_final: 0.8624 (t0) REVERT: A 296 LEU cc_start: 0.9014 (mm) cc_final: 0.8629 (tt) REVERT: A 317 ARG cc_start: 0.8754 (mtm110) cc_final: 0.8511 (mtm180) REVERT: A 392 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8632 (mt-10) REVERT: G 14 LYS cc_start: 0.9137 (mmmm) cc_final: 0.8815 (mmpt) REVERT: G 20 LYS cc_start: 0.8857 (mtmp) cc_final: 0.8422 (mtmm) REVERT: G 21 MET cc_start: 0.9055 (tpp) cc_final: 0.8612 (ttt) REVERT: G 58 GLU cc_start: 0.8695 (pm20) cc_final: 0.8376 (pm20) REVERT: S 73 ASP cc_start: 0.8495 (t70) cc_final: 0.7686 (t0) REVERT: S 186 GLN cc_start: 0.8865 (tt0) cc_final: 0.8599 (pt0) REVERT: N 46 GLU cc_start: 0.8560 (pt0) cc_final: 0.8340 (pt0) REVERT: N 73 ASP cc_start: 0.7697 (t70) cc_final: 0.7086 (t0) REVERT: N 83 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8739 (mtp) outliers start: 18 outliers final: 10 residues processed: 160 average time/residue: 0.6632 time to fit residues: 112.7928 Evaluate side-chains 161 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 80 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 0.0770 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 ASN S 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.082334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.055873 restraints weight = 22634.517| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 3.32 r_work: 0.2608 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10114 Z= 0.126 Angle : 0.617 10.424 13715 Z= 0.311 Chirality : 0.042 0.176 1539 Planarity : 0.004 0.059 1748 Dihedral : 3.911 21.346 1387 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.13 % Allowed : 19.23 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 are not related in a simple way. whole: 0.92 (0.23), residues: 1245 helix: 1.97 (0.26), residues: 394 sheet: 0.95 (0.28), residues: 324 loop : -0.66 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 105 TYR 0.015 0.001 TYR S 190 PHE 0.011 0.001 PHE A 212 TRP 0.022 0.001 TRP R 193 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00297 (10107) covalent geometry : angle 0.61644 (13703) SS BOND : bond 0.00405 ( 6) SS BOND : angle 0.86845 ( 12) hydrogen bonds : bond 0.03726 ( 459) hydrogen bonds : angle 4.01797 ( 1293) Misc. bond : bond 0.00007 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: R 85 ASP cc_start: 0.7923 (t70) cc_final: 0.7645 (t70) REVERT: R 100 LYS cc_start: 0.8689 (tppt) cc_final: 0.8135 (mttm) REVERT: R 311 MET cc_start: 0.8721 (mtp) cc_final: 0.8452 (ttm) REVERT: R 323 TRP cc_start: 0.8230 (m100) cc_final: 0.7816 (m-10) REVERT: B 10 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8855 (mm-30) REVERT: B 15 LYS cc_start: 0.8932 (mmmm) cc_final: 0.8714 (tptt) REVERT: B 25 CYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8031 (t) REVERT: B 59 TYR cc_start: 0.9182 (OUTLIER) cc_final: 0.8057 (m-80) REVERT: B 217 MET cc_start: 0.8774 (ptm) cc_final: 0.8100 (ppp) REVERT: B 312 ASP cc_start: 0.9065 (t0) cc_final: 0.8646 (t0) REVERT: A 296 LEU cc_start: 0.9038 (mm) cc_final: 0.8643 (tt) REVERT: A 317 ARG cc_start: 0.8772 (mtm110) cc_final: 0.8482 (mtm180) REVERT: A 392 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8630 (mt-10) REVERT: G 14 LYS cc_start: 0.9133 (mmmm) cc_final: 0.8806 (mmpt) REVERT: G 20 LYS cc_start: 0.8860 (mtmp) cc_final: 0.8454 (mtmm) REVERT: G 21 MET cc_start: 0.9057 (tpp) cc_final: 0.8623 (ttt) REVERT: G 58 GLU cc_start: 0.8630 (pm20) cc_final: 0.8393 (pm20) REVERT: S 73 ASP cc_start: 0.8496 (t70) cc_final: 0.7605 (t0) REVERT: S 76 LYS cc_start: 0.9024 (ptpp) cc_final: 0.8629 (ptpp) REVERT: S 186 GLN cc_start: 0.8817 (tt0) cc_final: 0.8555 (pt0) REVERT: N 83 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8757 (mtp) outliers start: 12 outliers final: 8 residues processed: 157 average time/residue: 0.6276 time to fit residues: 104.6616 Evaluate side-chains 157 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 80 HIS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 26 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.080858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.054448 restraints weight = 22780.366| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 3.31 r_work: 0.2577 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10114 Z= 0.174 Angle : 0.640 11.256 13715 Z= 0.324 Chirality : 0.043 0.164 1539 Planarity : 0.004 0.060 1748 Dihedral : 4.011 22.832 1387 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.41 % Allowed : 18.94 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 are not related in a simple way. whole: 0.89 (0.23), residues: 1245 helix: 1.92 (0.26), residues: 395 sheet: 0.94 (0.28), residues: 324 loop : -0.66 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 105 TYR 0.015 0.001 TYR S 190 PHE 0.011 0.001 PHE S 203 TRP 0.022 0.001 TRP R 193 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00413 (10107) covalent geometry : angle 0.63979 (13703) SS BOND : bond 0.00498 ( 6) SS BOND : angle 1.03901 ( 12) hydrogen bonds : bond 0.04138 ( 459) hydrogen bonds : angle 4.12579 ( 1293) Misc. bond : bond 0.00012 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3782.72 seconds wall clock time: 65 minutes 5.72 seconds (3905.72 seconds total)