Starting phenix.real_space_refine on Mon Jul 28 00:27:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kh0_22872/07_2025/7kh0_22872.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kh0_22872/07_2025/7kh0_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_22872/07_2025/7kh0_22872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kh0_22872/07_2025/7kh0_22872.map" model { file = "/net/cci-nas-00/data/ceres_data/7kh0_22872/07_2025/7kh0_22872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kh0_22872/07_2025/7kh0_22872.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1, 'HIS:plan': 1} 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: 6.39, per 1000 atoms: 0.65 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: 2.88 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.19 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: 3.13 Time building geometry restraints manager: 3.21 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: 1.110 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 26.960 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.260 ------------------------------------------------------------------------------- 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 : 6.31 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (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 TRP 0.011 0.001 TRP B 332 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.001 PHE R 77 TYR 0.016 0.001 TYR S 190 ARG 0.009 0.000 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.18098 ( 459) hydrogen bonds : angle 6.74023 ( 1293) SS BOND : bond 0.00357 ( 6) SS BOND : angle 1.24267 ( 12) covalent geometry : bond 0.00493 (10107) covalent geometry : angle 0.75839 (13703) 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 : 1.160 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: 1.4439 time to fit residues: 303.2869 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 : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 96 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.082571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.056169 restraints weight = 22304.091| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 3.29 r_work: 0.2613 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10114 Z= 0.126 Angle : 0.586 7.750 13715 Z= 0.305 Chirality : 0.043 0.170 1539 Planarity : 0.004 0.044 1748 Dihedral : 4.314 34.331 1387 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.60 % Allowed : 10.56 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.23), residues: 1245 helix: 1.70 (0.26), residues: 385 sheet: 0.50 (0.28), residues: 339 loop : -0.91 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 193 HIS 0.003 0.001 HIS A 357 PHE 0.011 0.001 PHE S 203 TYR 0.026 0.001 TYR S 190 ARG 0.008 0.001 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.04502 ( 459) hydrogen bonds : angle 4.68975 ( 1293) SS BOND : bond 0.00353 ( 6) SS BOND : angle 1.23568 ( 12) covalent geometry : bond 0.00278 (10107) covalent geometry : angle 0.58559 (13703) Misc. bond : bond 0.00025 ( 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 180 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 136 ASP cc_start: 0.8755 (t0) cc_final: 0.8497 (t0) REVERT: B 10 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8734 (mm-30) REVERT: B 15 LYS cc_start: 0.8908 (mmmm) cc_final: 0.8596 (tptt) REVERT: B 262 MET cc_start: 0.9278 (ttp) cc_final: 0.9022 (ttm) REVERT: B 312 ASP cc_start: 0.9035 (t0) cc_final: 0.8662 (t0) REVERT: G 20 LYS cc_start: 0.9048 (tppp) cc_final: 0.8554 (mtmp) REVERT: G 21 MET cc_start: 0.9013 (tpp) cc_final: 0.8627 (ttt) REVERT: G 22 GLU cc_start: 0.8841 (tt0) cc_final: 0.8457 (tt0) REVERT: G 58 GLU cc_start: 0.8577 (pm20) cc_final: 0.8360 (pm20) REVERT: S 73 ASP cc_start: 0.8431 (t70) cc_final: 0.7763 (t0) REVERT: N 39 GLN cc_start: 0.9113 (tm-30) cc_final: 0.8887 (tp40) REVERT: N 73 ASP cc_start: 0.7625 (t70) cc_final: 0.6984 (t0) REVERT: N 83 MET cc_start: 0.9327 (OUTLIER) cc_final: 0.8795 (mtp) outliers start: 17 outliers final: 6 residues processed: 172 average time/residue: 1.7652 time to fit residues: 321.8103 Evaluate side-chains 152 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 1.387 ------------------------------------------------------------------------------- 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 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 62 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 56 optimal weight: 0.0000 chunk 38 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 67 optimal weight: 0.0020 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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 A 294 GLN A 371 ASN ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN G 24 ASN S 13 GLN S 186 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.084267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.057848 restraints weight = 22666.896| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.30 r_work: 0.2658 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2051 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= 0.101 Angle : 0.540 7.645 13715 Z= 0.276 Chirality : 0.041 0.148 1539 Planarity : 0.004 0.042 1748 Dihedral : 3.967 26.333 1387 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.70 % Allowed : 11.88 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.23), residues: 1245 helix: 1.92 (0.26), residues: 385 sheet: 0.73 (0.28), residues: 336 loop : -0.82 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 193 HIS 0.002 0.000 HIS A 220 PHE 0.011 0.001 PHE A 212 TYR 0.018 0.001 TYR S 190 ARG 0.010 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03662 ( 459) hydrogen bonds : angle 4.19426 ( 1293) SS BOND : bond 0.00314 ( 6) SS BOND : angle 0.93903 ( 12) covalent geometry : bond 0.00222 (10107) covalent geometry : angle 0.53937 (13703) Misc. bond : bond 0.00002 ( 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 189 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: R 85 ASP cc_start: 0.7853 (t70) cc_final: 0.7526 (t70) REVERT: R 100 LYS cc_start: 0.8812 (mmtm) cc_final: 0.8269 (mttm) REVERT: R 136 ASP cc_start: 0.8786 (t0) cc_final: 0.8528 (OUTLIER) REVERT: B 10 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8722 (mm-30) REVERT: B 15 LYS cc_start: 0.8908 (mmmm) cc_final: 0.8617 (tptt) REVERT: B 59 TYR cc_start: 0.9230 (OUTLIER) cc_final: 0.7807 (m-80) REVERT: B 217 MET cc_start: 0.8179 (ptm) cc_final: 0.7478 (pp-130) REVERT: B 312 ASP cc_start: 0.9035 (t0) cc_final: 0.8684 (t0) REVERT: A 296 LEU cc_start: 0.9037 (mm) cc_final: 0.8566 (tt) REVERT: G 14 LYS cc_start: 0.9171 (mmmm) cc_final: 0.8834 (mmpt) REVERT: G 20 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8617 (mtmp) REVERT: G 21 MET cc_start: 0.9007 (tpp) cc_final: 0.8681 (ttt) REVERT: G 22 GLU cc_start: 0.8851 (tt0) cc_final: 0.8564 (tt0) REVERT: G 58 GLU cc_start: 0.8433 (pm20) cc_final: 0.8151 (pm20) REVERT: S 3 GLN cc_start: 0.8207 (tp40) cc_final: 0.7972 (tp-100) REVERT: S 43 LYS cc_start: 0.9230 (mmtm) cc_final: 0.8991 (mmpt) REVERT: S 73 ASP cc_start: 0.8497 (t70) cc_final: 0.7668 (t0) REVERT: S 76 LYS cc_start: 0.9081 (ptpp) cc_final: 0.8742 (ptpp) REVERT: N 39 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8761 (tp40) REVERT: N 73 ASP cc_start: 0.7729 (t70) cc_final: 0.7070 (t0) REVERT: N 83 MET cc_start: 0.9292 (OUTLIER) cc_final: 0.8830 (mtp) REVERT: N 90 ASP cc_start: 0.8970 (m-30) cc_final: 0.8651 (m-30) outliers start: 18 outliers final: 6 residues processed: 180 average time/residue: 1.3280 time to fit residues: 255.3160 Evaluate side-chains 163 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 28 ILE 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 41 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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** B 88 ASN ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.080821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.054443 restraints weight = 22769.022| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 3.29 r_work: 0.2572 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10114 Z= 0.191 Angle : 0.578 7.638 13715 Z= 0.300 Chirality : 0.043 0.149 1539 Planarity : 0.004 0.042 1748 Dihedral : 4.148 27.340 1387 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.98 % Allowed : 14.04 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.23), residues: 1245 helix: 1.96 (0.26), residues: 386 sheet: 0.75 (0.28), residues: 336 loop : -0.83 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 193 HIS 0.007 0.001 HIS A 357 PHE 0.014 0.001 PHE S 203 TYR 0.018 0.001 TYR S 190 ARG 0.007 0.000 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.04536 ( 459) hydrogen bonds : angle 4.32312 ( 1293) SS BOND : bond 0.00497 ( 6) SS BOND : angle 1.26393 ( 12) covalent geometry : bond 0.00450 (10107) covalent geometry : angle 0.57659 (13703) Misc. bond : bond 0.00023 ( 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 171 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 1.244 Fit side-chains revert: symmetry clash REVERT: R 85 ASP cc_start: 0.7979 (t70) cc_final: 0.7681 (t70) REVERT: R 136 ASP cc_start: 0.8847 (t0) cc_final: 0.8591 (t0) REVERT: B 10 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8782 (mm-30) REVERT: B 15 LYS cc_start: 0.8916 (mmmm) cc_final: 0.8655 (tptt) REVERT: B 59 TYR cc_start: 0.9346 (OUTLIER) cc_final: 0.8166 (m-80) REVERT: B 214 ARG cc_start: 0.9107 (mmm-85) cc_final: 0.8871 (mmm-85) REVERT: B 217 MET cc_start: 0.8396 (ptm) cc_final: 0.7877 (ppp) REVERT: B 312 ASP cc_start: 0.9016 (t0) cc_final: 0.8639 (t0) REVERT: A 392 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8653 (mt-10) REVERT: G 14 LYS cc_start: 0.9180 (mmmm) cc_final: 0.8832 (mmpt) REVERT: G 20 LYS cc_start: 0.9025 (tppp) cc_final: 0.8613 (mtmp) REVERT: G 21 MET cc_start: 0.9068 (tpp) cc_final: 0.8686 (ttt) REVERT: G 58 GLU cc_start: 0.8587 (pm20) cc_final: 0.8282 (pm20) REVERT: S 73 ASP cc_start: 0.8512 (t70) cc_final: 0.7692 (t0) REVERT: S 76 LYS cc_start: 0.9017 (ptpp) cc_final: 0.8690 (ptpp) REVERT: S 244 LYS cc_start: 0.8228 (ttpp) cc_final: 0.7848 (ttpt) REVERT: S 246 GLU cc_start: 0.7312 (mp0) cc_final: 0.6939 (mp0) REVERT: N 73 ASP cc_start: 0.7773 (t70) cc_final: 0.7131 (t0) REVERT: N 83 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.8808 (mtp) outliers start: 21 outliers final: 9 residues processed: 160 average time/residue: 1.4310 time to fit residues: 243.7984 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 : 1.099 ------------------------------------------------------------------------------- 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 392 GLU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 6 GLU 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 100 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 74 optimal weight: 0.0970 chunk 36 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 S 13 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.082689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.056227 restraints weight = 22503.062| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 3.31 r_work: 0.2615 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10114 Z= 0.112 Angle : 0.541 8.354 13715 Z= 0.277 Chirality : 0.041 0.133 1539 Planarity : 0.004 0.041 1748 Dihedral : 3.908 24.397 1387 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.07 % Allowed : 15.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.23), residues: 1245 helix: 2.03 (0.26), residues: 392 sheet: 0.89 (0.28), residues: 326 loop : -0.77 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 323 HIS 0.003 0.001 HIS A 357 PHE 0.010 0.001 PHE S 203 TYR 0.018 0.001 TYR S 190 ARG 0.011 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 459) hydrogen bonds : angle 4.05708 ( 1293) SS BOND : bond 0.00375 ( 6) SS BOND : angle 0.92257 ( 12) covalent geometry : bond 0.00256 (10107) covalent geometry : angle 0.54098 (13703) Misc. bond : bond 0.00007 ( 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 182 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 85 ASP cc_start: 0.7959 (t70) cc_final: 0.7627 (t70) REVERT: R 100 LYS cc_start: 0.8706 (tppt) cc_final: 0.8149 (ttmp) REVERT: R 136 ASP cc_start: 0.8746 (t0) cc_final: 0.8532 (t0) REVERT: R 323 TRP cc_start: 0.8027 (m100) cc_final: 0.7645 (m-10) REVERT: B 10 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8749 (mm-30) REVERT: B 15 LYS cc_start: 0.8914 (mmmm) cc_final: 0.8661 (tptt) REVERT: B 59 TYR cc_start: 0.9236 (OUTLIER) cc_final: 0.7899 (m-80) REVERT: B 217 MET cc_start: 0.8450 (ptm) cc_final: 0.7865 (ppp) REVERT: B 312 ASP cc_start: 0.9039 (t0) cc_final: 0.8656 (t0) REVERT: A 296 LEU cc_start: 0.9035 (mm) cc_final: 0.8600 (tt) REVERT: A 317 ARG cc_start: 0.8798 (mtm110) cc_final: 0.8560 (mpp-170) REVERT: A 392 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8649 (mt-10) REVERT: G 14 LYS cc_start: 0.9157 (mmmm) cc_final: 0.8816 (mmpt) REVERT: G 17 GLU cc_start: 0.9327 (tp30) cc_final: 0.9016 (mm-30) REVERT: G 20 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8676 (mtmp) REVERT: G 21 MET cc_start: 0.9065 (tpp) cc_final: 0.8695 (ttt) REVERT: S 43 LYS cc_start: 0.9148 (mmtm) cc_final: 0.8920 (mmpt) REVERT: S 73 ASP cc_start: 0.8457 (t70) cc_final: 0.7741 (t0) REVERT: S 244 LYS cc_start: 0.8177 (ttpp) cc_final: 0.7774 (ttpt) REVERT: S 246 GLU cc_start: 0.7168 (mp0) cc_final: 0.6783 (mp0) REVERT: N 73 ASP cc_start: 0.7650 (t70) cc_final: 0.7022 (t0) REVERT: N 83 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8813 (mtp) outliers start: 22 outliers final: 10 residues processed: 170 average time/residue: 2.1583 time to fit residues: 391.5565 Evaluate side-chains 161 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 209 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 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 5 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 53 optimal weight: 0.3980 chunk 0 optimal weight: 20.0000 chunk 119 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.081710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.055188 restraints weight = 22490.989| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 3.31 r_work: 0.2588 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10114 Z= 0.147 Angle : 0.562 8.101 13715 Z= 0.289 Chirality : 0.042 0.150 1539 Planarity : 0.004 0.041 1748 Dihedral : 3.914 22.882 1387 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.89 % Allowed : 16.49 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.23), residues: 1245 helix: 2.07 (0.26), residues: 392 sheet: 0.97 (0.28), residues: 323 loop : -0.76 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 193 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE S 203 TYR 0.017 0.001 TYR S 190 ARG 0.011 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 459) hydrogen bonds : angle 4.06564 ( 1293) SS BOND : bond 0.00465 ( 6) SS BOND : angle 1.03710 ( 12) covalent geometry : bond 0.00345 (10107) covalent geometry : angle 0.56108 (13703) Misc. bond : bond 0.00016 ( 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 169 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 1.216 Fit side-chains revert: symmetry clash REVERT: R 85 ASP cc_start: 0.8021 (t70) cc_final: 0.7739 (t70) REVERT: R 100 LYS cc_start: 0.8707 (tppt) cc_final: 0.8146 (ttmp) REVERT: R 136 ASP cc_start: 0.8755 (t0) cc_final: 0.8541 (t0) REVERT: R 311 MET cc_start: 0.8703 (mtp) cc_final: 0.8375 (ttm) REVERT: R 323 TRP cc_start: 0.8076 (m100) cc_final: 0.7702 (m-10) REVERT: B 10 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8790 (mm-30) REVERT: B 15 LYS cc_start: 0.8923 (mmmm) cc_final: 0.8672 (tptt) REVERT: B 59 TYR cc_start: 0.9304 (OUTLIER) cc_final: 0.8077 (m-80) REVERT: B 217 MET cc_start: 0.8482 (ptm) cc_final: 0.7894 (ppp) REVERT: B 312 ASP cc_start: 0.9029 (t0) cc_final: 0.8635 (t0) REVERT: A 296 LEU cc_start: 0.9037 (mm) cc_final: 0.8619 (tt) REVERT: A 392 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8624 (mt-10) REVERT: G 14 LYS cc_start: 0.9144 (mmmm) cc_final: 0.8811 (mmpt) REVERT: G 20 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8719 (mtmp) REVERT: G 21 MET cc_start: 0.9044 (tpp) cc_final: 0.8589 (ttt) REVERT: S 43 LYS cc_start: 0.9116 (mmtm) cc_final: 0.8869 (mmpt) REVERT: S 73 ASP cc_start: 0.8434 (t70) cc_final: 0.7439 (t0) REVERT: S 76 LYS cc_start: 0.8961 (ptpp) cc_final: 0.8457 (ptpp) REVERT: S 234 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8652 (pt0) REVERT: S 244 LYS cc_start: 0.8183 (ttpp) cc_final: 0.7781 (ttpt) REVERT: S 246 GLU cc_start: 0.7064 (mp0) cc_final: 0.6732 (mp0) REVERT: N 73 ASP cc_start: 0.7650 (t70) cc_final: 0.7016 (t0) REVERT: N 83 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8740 (mtp) outliers start: 20 outliers final: 10 residues processed: 159 average time/residue: 1.4037 time to fit residues: 237.6715 Evaluate side-chains 160 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 120 MET 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 R residue 209 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 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 83 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 N 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.082946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.056397 restraints weight = 22774.383| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 3.35 r_work: 0.2614 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10114 Z= 0.115 Angle : 0.562 9.307 13715 Z= 0.286 Chirality : 0.041 0.134 1539 Planarity : 0.004 0.048 1748 Dihedral : 3.796 20.768 1387 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.98 % Allowed : 17.06 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.23), residues: 1245 helix: 2.11 (0.26), residues: 392 sheet: 0.98 (0.28), residues: 334 loop : -0.71 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 193 HIS 0.003 0.001 HIS A 357 PHE 0.010 0.001 PHE S 203 TYR 0.017 0.001 TYR S 190 ARG 0.013 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 459) hydrogen bonds : angle 3.92701 ( 1293) SS BOND : bond 0.00427 ( 6) SS BOND : angle 0.92260 ( 12) covalent geometry : bond 0.00265 (10107) covalent geometry : angle 0.56161 (13703) Misc. bond : bond 0.00009 ( 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 169 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 85 ASP cc_start: 0.7961 (t70) cc_final: 0.7661 (t70) REVERT: R 100 LYS cc_start: 0.8691 (tppt) cc_final: 0.8133 (mttm) REVERT: R 136 ASP cc_start: 0.8730 (t0) cc_final: 0.8518 (t0) REVERT: R 311 MET cc_start: 0.8701 (mtp) cc_final: 0.8381 (ttm) REVERT: R 323 TRP cc_start: 0.8172 (m100) cc_final: 0.7786 (m-10) REVERT: B 10 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8801 (mm-30) REVERT: B 12 GLU cc_start: 0.8514 (pp20) cc_final: 0.8311 (pp20) REVERT: B 15 LYS cc_start: 0.8923 (mmmm) cc_final: 0.8704 (tptt) REVERT: B 25 CYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8004 (t) REVERT: B 59 TYR cc_start: 0.9242 (OUTLIER) cc_final: 0.8079 (m-80) REVERT: B 217 MET cc_start: 0.8507 (ptm) cc_final: 0.7918 (ppp) REVERT: B 312 ASP cc_start: 0.9040 (t0) cc_final: 0.8657 (t0) REVERT: A 296 LEU cc_start: 0.9040 (mm) cc_final: 0.8636 (tt) REVERT: A 365 CYS cc_start: 0.8145 (m) cc_final: 0.6729 (t) REVERT: A 392 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8656 (mt-10) REVERT: G 14 LYS cc_start: 0.9131 (mmmm) cc_final: 0.8801 (mmpt) REVERT: G 17 GLU cc_start: 0.9293 (tp30) cc_final: 0.8999 (mm-30) REVERT: G 20 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8761 (mtmp) REVERT: G 21 MET cc_start: 0.9056 (tpp) cc_final: 0.8654 (ttt) REVERT: G 32 LYS cc_start: 0.8632 (ttmm) cc_final: 0.8384 (ttpp) REVERT: S 43 LYS cc_start: 0.9105 (mmtm) cc_final: 0.8855 (mmpt) REVERT: S 73 ASP cc_start: 0.8432 (t70) cc_final: 0.7543 (t0) REVERT: S 76 LYS cc_start: 0.8908 (ptpp) cc_final: 0.8457 (ptpp) REVERT: S 234 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8615 (pt0) REVERT: N 73 ASP cc_start: 0.7641 (t70) cc_final: 0.7016 (t0) outliers start: 21 outliers final: 9 residues processed: 160 average time/residue: 1.3502 time to fit residues: 230.3713 Evaluate side-chains 157 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 209 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 16 VAL Chi-restraints excluded: chain G residue 20 LYS 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 89 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 chunk 79 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 119 GLN G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.079935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.053699 restraints weight = 22754.378| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 3.32 r_work: 0.2540 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10114 Z= 0.230 Angle : 0.633 9.318 13715 Z= 0.326 Chirality : 0.044 0.157 1539 Planarity : 0.004 0.050 1748 Dihedral : 4.120 24.908 1387 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.89 % Allowed : 18.00 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.23), residues: 1245 helix: 1.96 (0.26), residues: 393 sheet: 0.95 (0.28), residues: 323 loop : -0.76 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 193 HIS 0.006 0.001 HIS A 357 PHE 0.011 0.001 PHE S 203 TYR 0.015 0.001 TYR S 190 ARG 0.012 0.001 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.04631 ( 459) hydrogen bonds : angle 4.25058 ( 1293) SS BOND : bond 0.00536 ( 6) SS BOND : angle 1.18985 ( 12) covalent geometry : bond 0.00543 (10107) covalent geometry : angle 0.63181 (13703) Misc. bond : bond 0.00020 ( 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 167 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 85 ASP cc_start: 0.7973 (t70) cc_final: 0.7699 (t70) REVERT: R 100 LYS cc_start: 0.8692 (tppt) cc_final: 0.8139 (mttm) REVERT: R 136 ASP cc_start: 0.8821 (t0) cc_final: 0.8604 (t0) REVERT: R 323 TRP cc_start: 0.8200 (m100) cc_final: 0.7814 (m-10) REVERT: B 10 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8790 (mm-30) REVERT: B 15 LYS cc_start: 0.8920 (mmmm) cc_final: 0.8686 (tptt) REVERT: B 59 TYR cc_start: 0.9360 (OUTLIER) cc_final: 0.8339 (m-80) REVERT: B 214 ARG cc_start: 0.9119 (mmm-85) cc_final: 0.8914 (mmm-85) REVERT: B 217 MET cc_start: 0.8650 (ptm) cc_final: 0.8045 (ppp) REVERT: B 254 ASP cc_start: 0.8644 (t0) cc_final: 0.7986 (t0) REVERT: B 312 ASP cc_start: 0.9007 (t0) cc_final: 0.8622 (t0) REVERT: A 296 LEU cc_start: 0.9070 (mm) cc_final: 0.8685 (tt) REVERT: A 317 ARG cc_start: 0.8776 (mtm110) cc_final: 0.8236 (ptp90) REVERT: A 392 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8645 (mt-10) REVERT: G 14 LYS cc_start: 0.9159 (mmmm) cc_final: 0.8837 (mmpt) REVERT: G 20 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8748 (mtmp) REVERT: G 21 MET cc_start: 0.9041 (tpp) cc_final: 0.8567 (ttt) REVERT: S 73 ASP cc_start: 0.8482 (t70) cc_final: 0.7571 (t0) REVERT: S 76 LYS cc_start: 0.8894 (ptpp) cc_final: 0.8438 (ptpp) REVERT: S 234 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8678 (pt0) REVERT: N 73 ASP cc_start: 0.7729 (t70) cc_final: 0.7032 (t0) outliers start: 20 outliers final: 13 residues processed: 157 average time/residue: 1.3834 time to fit residues: 231.3597 Evaluate side-chains 160 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 120 MET 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 R residue 209 ILE 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 20 LYS 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 20 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.082376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.055901 restraints weight = 22687.341| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 3.32 r_work: 0.2607 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10114 Z= 0.124 Angle : 0.600 8.704 13715 Z= 0.305 Chirality : 0.042 0.136 1539 Planarity : 0.004 0.055 1748 Dihedral : 3.905 21.142 1387 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.23 % Allowed : 18.66 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.23), residues: 1245 helix: 2.03 (0.26), residues: 392 sheet: 0.94 (0.28), residues: 323 loop : -0.70 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 193 HIS 0.003 0.001 HIS A 357 PHE 0.010 0.001 PHE A 212 TYR 0.015 0.001 TYR S 190 ARG 0.014 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03688 ( 459) hydrogen bonds : angle 3.98857 ( 1293) SS BOND : bond 0.00383 ( 6) SS BOND : angle 0.86861 ( 12) covalent geometry : bond 0.00291 (10107) covalent geometry : angle 0.59923 (13703) Misc. bond : bond 0.00008 ( 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 161 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 1.773 Fit side-chains revert: symmetry clash REVERT: R 85 ASP cc_start: 0.7919 (t70) cc_final: 0.7634 (t70) REVERT: R 100 LYS cc_start: 0.8662 (tppt) cc_final: 0.8093 (mttm) REVERT: R 136 ASP cc_start: 0.8736 (t0) cc_final: 0.8527 (t0) REVERT: R 311 MET cc_start: 0.8699 (mtp) cc_final: 0.8393 (mtm) REVERT: R 323 TRP cc_start: 0.8172 (m100) cc_final: 0.7851 (m-10) REVERT: B 10 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8835 (mm-30) REVERT: B 15 LYS cc_start: 0.8930 (mmmm) cc_final: 0.8702 (tptt) REVERT: B 25 CYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8015 (t) REVERT: B 59 TYR cc_start: 0.9246 (OUTLIER) cc_final: 0.8104 (m-80) REVERT: B 214 ARG cc_start: 0.9118 (mmm-85) cc_final: 0.8901 (mmm-85) REVERT: B 217 MET cc_start: 0.8598 (ptm) cc_final: 0.7914 (ppp) REVERT: B 312 ASP cc_start: 0.9029 (t0) cc_final: 0.8665 (t0) REVERT: A 296 LEU cc_start: 0.9047 (mm) cc_final: 0.8654 (tt) REVERT: A 317 ARG cc_start: 0.8785 (mtm110) cc_final: 0.8285 (ptp90) REVERT: A 365 CYS cc_start: 0.8219 (m) cc_final: 0.6901 (t) REVERT: A 392 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8612 (mt-10) REVERT: G 14 LYS cc_start: 0.9138 (mmmm) cc_final: 0.8809 (mmpt) REVERT: G 17 GLU cc_start: 0.9274 (tp30) cc_final: 0.9014 (mm-30) REVERT: G 20 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8753 (mtmp) REVERT: G 21 MET cc_start: 0.9050 (tpp) cc_final: 0.8615 (ttp) REVERT: S 43 LYS cc_start: 0.9006 (mmtm) cc_final: 0.8787 (mmpt) REVERT: S 73 ASP cc_start: 0.8424 (t70) cc_final: 0.7508 (t0) REVERT: S 76 LYS cc_start: 0.8898 (ptpp) cc_final: 0.8448 (ptpp) REVERT: S 234 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8656 (pt0) REVERT: N 46 GLU cc_start: 0.8475 (pt0) cc_final: 0.8249 (pt0) outliers start: 13 outliers final: 9 residues processed: 156 average time/residue: 1.5917 time to fit residues: 263.7595 Evaluate side-chains 154 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 R residue 209 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 16 VAL Chi-restraints excluded: chain G residue 20 LYS 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 35 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 92 GLN G 24 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.081255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.054819 restraints weight = 22637.689| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.31 r_work: 0.2585 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10114 Z= 0.159 Angle : 0.622 11.215 13715 Z= 0.315 Chirality : 0.043 0.137 1539 Planarity : 0.004 0.060 1748 Dihedral : 3.934 22.159 1387 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.23 % Allowed : 19.04 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.23), residues: 1245 helix: 1.99 (0.26), residues: 393 sheet: 1.00 (0.28), residues: 323 loop : -0.69 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 193 HIS 0.005 0.001 HIS A 357 PHE 0.010 0.001 PHE S 203 TYR 0.015 0.001 TYR S 190 ARG 0.014 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 459) hydrogen bonds : angle 4.04967 ( 1293) SS BOND : bond 0.00466 ( 6) SS BOND : angle 0.99319 ( 12) covalent geometry : bond 0.00378 (10107) covalent geometry : angle 0.62135 (13703) Misc. bond : bond 0.00011 ( 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 157 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 1.199 Fit side-chains revert: symmetry clash REVERT: R 85 ASP cc_start: 0.7963 (t70) cc_final: 0.7690 (t70) REVERT: R 100 LYS cc_start: 0.8641 (tppt) cc_final: 0.8069 (mttm) REVERT: R 136 ASP cc_start: 0.8791 (t0) cc_final: 0.8579 (t0) REVERT: R 311 MET cc_start: 0.8740 (mtp) cc_final: 0.8476 (mtm) REVERT: R 323 TRP cc_start: 0.8202 (m100) cc_final: 0.7828 (m-10) REVERT: B 10 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8832 (mm-30) REVERT: B 15 LYS cc_start: 0.8934 (mmmm) cc_final: 0.8699 (tptt) REVERT: B 25 CYS cc_start: 0.8613 (m) cc_final: 0.8032 (t) REVERT: B 59 TYR cc_start: 0.9306 (OUTLIER) cc_final: 0.8240 (m-80) REVERT: B 214 ARG cc_start: 0.9113 (mmm-85) cc_final: 0.8878 (mmm-85) REVERT: B 217 MET cc_start: 0.8629 (ptm) cc_final: 0.7915 (ppp) REVERT: B 254 ASP cc_start: 0.8568 (t0) cc_final: 0.7898 (t0) REVERT: B 312 ASP cc_start: 0.9027 (t0) cc_final: 0.8658 (t0) REVERT: A 296 LEU cc_start: 0.9048 (mm) cc_final: 0.8656 (tt) REVERT: A 317 ARG cc_start: 0.8797 (mtm110) cc_final: 0.8320 (ptp90) REVERT: A 365 CYS cc_start: 0.8245 (m) cc_final: 0.7243 (p) REVERT: A 392 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8625 (mt-10) REVERT: G 14 LYS cc_start: 0.9169 (mmmm) cc_final: 0.8855 (mmpt) REVERT: G 21 MET cc_start: 0.9049 (tpp) cc_final: 0.8589 (ttt) REVERT: S 43 LYS cc_start: 0.8994 (mmtm) cc_final: 0.8720 (mppt) REVERT: S 73 ASP cc_start: 0.8461 (t70) cc_final: 0.7552 (t0) REVERT: S 76 LYS cc_start: 0.8850 (ptpp) cc_final: 0.8389 (ptpp) REVERT: S 234 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8654 (pt0) REVERT: N 46 GLU cc_start: 0.8493 (pt0) cc_final: 0.8263 (pt0) outliers start: 13 outliers final: 10 residues processed: 153 average time/residue: 2.0873 time to fit residues: 339.5798 Evaluate side-chains 154 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 1.251 ------------------------------------------------------------------------------- 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 120 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 209 ILE 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 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 93 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 107 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 S 186 GLN N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.081825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.055413 restraints weight = 22780.239| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 3.32 r_work: 0.2598 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10114 Z= 0.141 Angle : 0.621 10.705 13715 Z= 0.313 Chirality : 0.042 0.134 1539 Planarity : 0.004 0.063 1748 Dihedral : 3.911 21.622 1387 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.94 % Allowed : 19.60 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.23), residues: 1245 helix: 1.98 (0.26), residues: 394 sheet: 1.01 (0.28), residues: 323 loop : -0.67 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 193 HIS 0.004 0.001 HIS A 357 PHE 0.009 0.001 PHE S 203 TYR 0.015 0.001 TYR S 190 ARG 0.015 0.001 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 459) hydrogen bonds : angle 4.01127 ( 1293) SS BOND : bond 0.00439 ( 6) SS BOND : angle 0.90974 ( 12) covalent geometry : bond 0.00335 (10107) covalent geometry : angle 0.62105 (13703) Misc. bond : bond 0.00009 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8413.65 seconds wall clock time: 151 minutes 13.37 seconds (9073.37 seconds total)