Starting phenix.real_space_refine on Fri Feb 14 06:06:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kh0_22872/02_2025/7kh0_22872.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kh0_22872/02_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_22872/02_2025/7kh0_22872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kh0_22872/02_2025/7kh0_22872.map" model { file = "/net/cci-nas-00/data/ceres_data/7kh0_22872/02_2025/7kh0_22872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kh0_22872/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.22, per 1000 atoms: 0.63 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: 2.66 Conformation dependent library (CDL) restraints added in 1.2 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: 1.13 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: 3.02 Time building geometry restraints manager: 3.05 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: 0.830 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 24.870 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.200 ------------------------------------------------------------------------------- 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 0.043 10107 Z= 0.320 Angle : 0.758 12.977 13703 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 *********************** 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 : 1.138 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: 1.4698 time to fit residues: 308.6452 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 : 1.109 ------------------------------------------------------------------------------- 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 = 35)----------------| | 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: 3.65 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 10107 Z= 0.179 Angle : 0.586 7.750 13703 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 *********************** 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 : 1.088 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: 0.9021 (ttm) REVERT: B 312 ASP cc_start: 0.9035 (t0) cc_final: 0.8662 (t0) REVERT: G 20 LYS cc_start: 0.9047 (tppp) cc_final: 0.8554 (mtmp) REVERT: G 21 MET cc_start: 0.9014 (tpp) cc_final: 0.8627 (ttt) REVERT: G 22 GLU cc_start: 0.8840 (tt0) cc_final: 0.8456 (tt0) REVERT: G 58 GLU cc_start: 0.8577 (pm20) cc_final: 0.8359 (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: 0.9326 (OUTLIER) cc_final: 0.8794 (mtp) outliers start: 17 outliers final: 6 residues processed: 172 average time/residue: 1.3645 time to fit residues: 249.9367 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 : 1.180 ------------------------------------------------------------------------------- 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: 0.6980 chunk 95 optimal weight: 0.0870 chunk 2 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.4562 ------------------------------------------------------------------------------- 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 = 0.3364 r_free = 0.3364 target = 0.084336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.057920 restraints weight = 22663.436| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 3.30 r_work: 0.2659 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10107 Z= 0.140 Angle : 0.541 7.613 13703 Z= 0.277 Chirality : 0.042 0.143 1539 Planarity : 0.004 0.044 1748 Dihedral : 3.971 26.386 1387 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.04 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: 1.91 (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 0.019 0.001 TRP R 193 HIS 0.002 0.000 HIS A 220 PHE 0.011 0.001 PHE S 203 TYR 0.018 0.001 TYR S 190 ARG 0.010 0.000 ARG N 105 *********************** 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 : 1.089 Fit side-chains revert: symmetry clash REVERT: R 85 ASP cc_start: 0.7852 (t70) cc_final: 0.7520 (t70) REVERT: R 100 LYS cc_start: 0.8811 (mmtm) cc_final: 0.8269 (mttm) REVERT: R 129 MET cc_start: 0.8619 (tpp) cc_final: 0.7958 (mmm) REVERT: R 136 ASP cc_start: 0.8778 (t0) cc_final: 0.8514 (OUTLIER) REVERT: B 10 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8724 (mm-30) REVERT: B 15 LYS cc_start: 0.8908 (mmmm) cc_final: 0.8618 (tptt) REVERT: B 59 TYR cc_start: 0.9231 (OUTLIER) cc_final: 0.7809 (m-80) REVERT: B 217 MET cc_start: 0.8184 (ptm) cc_final: 0.7481 (pp-130) REVERT: B 312 ASP cc_start: 0.9034 (t0) cc_final: 0.8682 (t0) REVERT: A 296 LEU cc_start: 0.9036 (mm) cc_final: 0.8565 (tt) REVERT: G 14 LYS cc_start: 0.9172 (mmmm) cc_final: 0.8834 (mmpt) REVERT: G 20 LYS cc_start: 0.9052 (tppp) cc_final: 0.8612 (mtmp) REVERT: G 21 MET cc_start: 0.9012 (tpp) cc_final: 0.8692 (ttt) REVERT: G 22 GLU cc_start: 0.8847 (tt0) cc_final: 0.8558 (tt0) REVERT: G 58 GLU cc_start: 0.8431 (pm20) cc_final: 0.8150 (pm20) REVERT: S 3 GLN cc_start: 0.8206 (tp40) cc_final: 0.7972 (tp-100) REVERT: S 43 LYS cc_start: 0.9241 (mmtm) cc_final: 0.9000 (mmpt) REVERT: S 73 ASP cc_start: 0.8499 (t70) cc_final: 0.7666 (t0) REVERT: S 76 LYS cc_start: 0.9086 (ptpp) cc_final: 0.8742 (ptpp) REVERT: N 39 GLN cc_start: 0.9061 (tm-30) cc_final: 0.8759 (tp40) REVERT: N 73 ASP cc_start: 0.7730 (t70) cc_final: 0.7068 (t0) REVERT: N 83 MET cc_start: 0.9292 (OUTLIER) cc_final: 0.8826 (mtp) REVERT: N 90 ASP cc_start: 0.8970 (m-30) cc_final: 0.8689 (m-30) outliers start: 18 outliers final: 6 residues processed: 180 average time/residue: 1.3200 time to fit residues: 253.7990 Evaluate side-chains 162 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 155 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 39 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.3285 r_free = 0.3285 target = 0.079840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.053537 restraints weight = 22874.895| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 3.28 r_work: 0.2550 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 10107 Z= 0.363 Angle : 0.604 7.778 13703 Z= 0.315 Chirality : 0.045 0.145 1539 Planarity : 0.004 0.042 1748 Dihedral : 4.279 29.476 1387 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.26 % Allowed : 14.14 % Favored : 83.60 % 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: 0.68 (0.23), residues: 1245 helix: 1.90 (0.26), residues: 386 sheet: 0.68 (0.28), residues: 338 loop : -0.82 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 193 HIS 0.007 0.001 HIS A 357 PHE 0.013 0.001 PHE S 203 TYR 0.018 0.001 TYR S 190 ARG 0.007 0.000 ARG G 13 *********************** 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 175 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: R 85 ASP cc_start: 0.8118 (t70) cc_final: 0.7823 (t70) REVERT: R 136 ASP cc_start: 0.8854 (t0) cc_final: 0.8598 (t0) REVERT: B 10 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8801 (mm-30) REVERT: B 15 LYS cc_start: 0.8918 (mmmm) cc_final: 0.8654 (tptt) REVERT: B 59 TYR cc_start: 0.9374 (OUTLIER) cc_final: 0.8255 (m-80) REVERT: B 217 MET cc_start: 0.8445 (ptm) cc_final: 0.7904 (ppp) REVERT: B 312 ASP cc_start: 0.9026 (t0) cc_final: 0.8622 (t0) REVERT: A 392 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8662 (mt-10) REVERT: G 14 LYS cc_start: 0.9187 (mmmm) cc_final: 0.8854 (mmpt) REVERT: G 20 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8615 (mtmp) REVERT: G 21 MET cc_start: 0.9063 (tpp) cc_final: 0.8665 (ttt) REVERT: G 22 GLU cc_start: 0.8925 (tt0) cc_final: 0.8713 (tt0) REVERT: G 58 GLU cc_start: 0.8640 (pm20) cc_final: 0.8331 (pm20) REVERT: S 73 ASP cc_start: 0.8520 (t70) cc_final: 0.7668 (t0) REVERT: S 76 LYS cc_start: 0.9025 (ptpp) cc_final: 0.8655 (ptpp) REVERT: S 244 LYS cc_start: 0.8240 (ttpp) cc_final: 0.7861 (ttpt) REVERT: S 246 GLU cc_start: 0.7291 (mp0) cc_final: 0.6903 (mp0) REVERT: N 73 ASP cc_start: 0.7769 (t70) cc_final: 0.7109 (t0) REVERT: N 83 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.8862 (mtp) outliers start: 24 outliers final: 12 residues processed: 162 average time/residue: 1.4086 time to fit residues: 243.2562 Evaluate side-chains 161 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 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 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 20 LYS 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: 8.9990 chunk 93 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 78 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 S 186 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.082941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.056594 restraints weight = 22483.123| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 3.30 r_work: 0.2619 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10107 Z= 0.156 Angle : 0.542 8.601 13703 Z= 0.277 Chirality : 0.041 0.133 1539 Planarity : 0.004 0.045 1748 Dihedral : 3.912 24.614 1387 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.17 % Allowed : 15.46 % Favored : 82.38 % 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: 0.81 (0.23), residues: 1245 helix: 2.00 (0.26), residues: 392 sheet: 0.90 (0.28), residues: 320 loop : -0.82 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 323 HIS 0.002 0.001 HIS A 220 PHE 0.010 0.001 PHE A 212 TYR 0.018 0.001 TYR S 190 ARG 0.010 0.000 ARG N 105 *********************** 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 186 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 1.203 Fit side-chains revert: symmetry clash REVERT: R 85 ASP cc_start: 0.7968 (t70) cc_final: 0.7644 (t70) REVERT: R 100 LYS cc_start: 0.8718 (tppt) cc_final: 0.8165 (ttmp) REVERT: R 136 ASP cc_start: 0.8732 (t0) cc_final: 0.8511 (t0) REVERT: R 323 TRP cc_start: 0.8068 (m100) cc_final: 0.7683 (m-10) REVERT: B 10 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8766 (mm-30) REVERT: B 15 LYS cc_start: 0.8910 (mmmm) cc_final: 0.8659 (tptt) REVERT: B 124 TYR cc_start: 0.9186 (m-80) cc_final: 0.8967 (m-80) REVERT: B 214 ARG cc_start: 0.9055 (mmm-85) cc_final: 0.8785 (mmm-85) REVERT: B 217 MET cc_start: 0.8526 (ptm) cc_final: 0.7952 (ppp) REVERT: B 312 ASP cc_start: 0.9031 (t0) cc_final: 0.8645 (t0) REVERT: A 296 LEU cc_start: 0.9034 (mm) cc_final: 0.8600 (tt) REVERT: A 317 ARG cc_start: 0.8796 (mtm110) cc_final: 0.8546 (mpp-170) REVERT: A 392 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8626 (mt-10) REVERT: G 14 LYS cc_start: 0.9149 (mmmm) cc_final: 0.8818 (mmpt) REVERT: G 20 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8688 (mtmp) REVERT: G 21 MET cc_start: 0.9066 (tpp) cc_final: 0.8653 (ttt) REVERT: G 58 GLU cc_start: 0.8536 (pm20) cc_final: 0.8309 (pm20) REVERT: S 43 LYS cc_start: 0.9138 (mmtm) cc_final: 0.8907 (mmpt) REVERT: S 73 ASP cc_start: 0.8447 (t70) cc_final: 0.7737 (t0) REVERT: S 244 LYS cc_start: 0.8127 (ttpp) cc_final: 0.7909 (tttt) REVERT: N 46 GLU cc_start: 0.8469 (pt0) cc_final: 0.8218 (pt0) REVERT: N 73 ASP cc_start: 0.7588 (t70) cc_final: 0.6963 (t0) REVERT: N 83 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8792 (mtp) outliers start: 23 outliers final: 8 residues processed: 173 average time/residue: 1.3616 time to fit residues: 251.0284 Evaluate side-chains 162 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 160 VAL Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain 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: 9.9990 chunk 78 optimal weight: 8.9990 chunk 85 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 0.0470 chunk 0 optimal weight: 20.0000 chunk 119 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- 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 = 0.3302 r_free = 0.3302 target = 0.081320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.054821 restraints weight = 22482.564| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 3.30 r_work: 0.2581 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10107 Z= 0.243 Angle : 0.570 8.116 13703 Z= 0.294 Chirality : 0.042 0.152 1539 Planarity : 0.004 0.042 1748 Dihedral : 3.950 23.342 1387 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.98 % Allowed : 16.87 % Favored : 81.15 % 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: 0.88 (0.23), residues: 1245 helix: 2.05 (0.26), residues: 392 sheet: 0.95 (0.28), residues: 323 loop : -0.79 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 193 HIS 0.005 0.001 HIS A 357 PHE 0.011 0.001 PHE S 203 TYR 0.018 0.001 TYR S 190 ARG 0.010 0.000 ARG N 105 *********************** 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 171 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: R 85 ASP cc_start: 0.8044 (t70) cc_final: 0.7750 (t70) REVERT: R 100 LYS cc_start: 0.8711 (tppt) cc_final: 0.8149 (ttmp) REVERT: R 136 ASP cc_start: 0.8786 (t0) cc_final: 0.8556 (t0) REVERT: R 311 MET cc_start: 0.8693 (mtp) cc_final: 0.8321 (ttm) REVERT: R 323 TRP cc_start: 0.8096 (m100) cc_final: 0.7730 (m-10) REVERT: B 10 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8785 (mm-30) REVERT: B 15 LYS cc_start: 0.8929 (mmmm) cc_final: 0.8677 (tptt) REVERT: B 59 TYR cc_start: 0.9229 (OUTLIER) cc_final: 0.8182 (m-80) REVERT: B 217 MET cc_start: 0.8536 (ptm) cc_final: 0.7943 (ppp) REVERT: B 312 ASP cc_start: 0.9026 (t0) cc_final: 0.8615 (t0) REVERT: A 296 LEU cc_start: 0.9046 (mm) cc_final: 0.8633 (tt) REVERT: A 392 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8647 (mt-10) REVERT: G 14 LYS cc_start: 0.9141 (mmmm) cc_final: 0.8811 (mmpt) REVERT: G 20 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8744 (mtmp) REVERT: G 21 MET cc_start: 0.9074 (tpp) cc_final: 0.8654 (ttt) REVERT: G 58 GLU cc_start: 0.8613 (pm20) cc_final: 0.8375 (pm20) REVERT: S 43 LYS cc_start: 0.9118 (mmtm) cc_final: 0.8870 (mmpt) REVERT: S 73 ASP cc_start: 0.8445 (t70) cc_final: 0.7576 (t0) REVERT: S 76 LYS cc_start: 0.8915 (ptpp) cc_final: 0.8506 (ptpp) REVERT: S 234 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8645 (pt0) REVERT: S 244 LYS cc_start: 0.8082 (ttpp) cc_final: 0.7731 (ttpt) REVERT: S 246 GLU cc_start: 0.6866 (mp0) cc_final: 0.6576 (mp0) REVERT: N 46 GLU cc_start: 0.8496 (pt0) cc_final: 0.8270 (pt0) REVERT: N 73 ASP cc_start: 0.7651 (t70) cc_final: 0.7011 (t0) REVERT: N 83 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8758 (mtp) outliers start: 21 outliers final: 10 residues processed: 160 average time/residue: 1.4023 time to fit residues: 239.0520 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 : 1.150 ------------------------------------------------------------------------------- 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 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 G residue 57 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 83 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 67 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.083496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.056995 restraints weight = 22666.542| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 3.34 r_work: 0.2630 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10107 Z= 0.150 Angle : 0.552 9.561 13703 Z= 0.282 Chirality : 0.041 0.132 1539 Planarity : 0.004 0.051 1748 Dihedral : 3.767 20.177 1387 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.70 % Allowed : 17.81 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.24), residues: 1245 helix: 2.14 (0.26), residues: 392 sheet: 0.95 (0.28), residues: 336 loop : -0.70 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 193 HIS 0.002 0.000 HIS A 220 PHE 0.010 0.001 PHE S 203 TYR 0.017 0.001 TYR S 190 ARG 0.013 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: R 85 ASP cc_start: 0.7986 (t70) cc_final: 0.7697 (t70) REVERT: R 100 LYS cc_start: 0.8692 (tppt) cc_final: 0.8131 (mttm) REVERT: R 136 ASP cc_start: 0.8726 (t0) cc_final: 0.8511 (t0) REVERT: R 311 MET cc_start: 0.8677 (mtp) cc_final: 0.8346 (ttm) REVERT: R 323 TRP cc_start: 0.8164 (m100) cc_final: 0.7811 (m-10) REVERT: B 10 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8835 (mm-30) REVERT: B 15 LYS cc_start: 0.8920 (mmmm) cc_final: 0.8699 (tptt) REVERT: B 25 CYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8024 (t) REVERT: B 59 TYR cc_start: 0.9142 (OUTLIER) cc_final: 0.8051 (m-80) REVERT: B 214 ARG cc_start: 0.9103 (mmm-85) cc_final: 0.8881 (mmm-85) REVERT: B 217 MET cc_start: 0.8572 (ptm) cc_final: 0.7992 (ppp) REVERT: B 312 ASP cc_start: 0.9051 (t0) cc_final: 0.8657 (t0) REVERT: A 296 LEU cc_start: 0.9049 (mm) cc_final: 0.8647 (tt) REVERT: A 392 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8663 (mt-10) REVERT: G 14 LYS cc_start: 0.9154 (mmmm) cc_final: 0.8821 (mmpt) REVERT: G 20 LYS cc_start: 0.9000 (tppp) cc_final: 0.8767 (mtmp) REVERT: G 21 MET cc_start: 0.9050 (tpp) cc_final: 0.8626 (ttt) REVERT: G 58 GLU cc_start: 0.8553 (pm20) cc_final: 0.8315 (pm20) REVERT: S 43 LYS cc_start: 0.9114 (mmtm) cc_final: 0.8867 (mmpt) REVERT: S 73 ASP cc_start: 0.8438 (t70) cc_final: 0.7545 (t0) REVERT: S 76 LYS cc_start: 0.8911 (ptpp) cc_final: 0.8457 (ptpp) REVERT: S 234 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8617 (pt0) REVERT: N 5 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8374 (tp40) REVERT: N 83 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8746 (mtp) outliers start: 18 outliers final: 9 residues processed: 160 average time/residue: 1.3793 time to fit residues: 234.9795 Evaluate side-chains 159 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 1.551 ------------------------------------------------------------------------------- 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 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 28 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 89 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 chunk 79 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 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 92 GLN R 119 GLN G 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.079660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.053360 restraints weight = 22832.893| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 3.29 r_work: 0.2546 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10107 Z= 0.352 Angle : 0.635 9.189 13703 Z= 0.327 Chirality : 0.044 0.159 1539 Planarity : 0.004 0.050 1748 Dihedral : 4.127 24.788 1387 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.60 % Allowed : 18.76 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.82 (0.23), residues: 1245 helix: 1.92 (0.26), residues: 393 sheet: 0.92 (0.28), residues: 324 loop : -0.77 (0.25), residues: 528 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 A 219 TYR 0.015 0.001 TYR S 190 ARG 0.012 0.001 ARG N 105 *********************** 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 164 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 85 ASP cc_start: 0.7998 (t70) cc_final: 0.7732 (t70) REVERT: R 100 LYS cc_start: 0.8700 (tppt) cc_final: 0.8136 (mttm) REVERT: R 136 ASP cc_start: 0.8828 (t0) cc_final: 0.8604 (t0) REVERT: R 323 TRP cc_start: 0.8212 (m100) cc_final: 0.7822 (m-10) REVERT: B 10 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8832 (mm-30) REVERT: B 15 LYS cc_start: 0.8924 (mmmm) cc_final: 0.8720 (tptt) REVERT: B 59 TYR cc_start: 0.9305 (OUTLIER) cc_final: 0.8295 (m-80) REVERT: B 214 ARG cc_start: 0.9110 (mmm-85) cc_final: 0.8892 (mmm-85) REVERT: B 217 MET cc_start: 0.8650 (ptm) cc_final: 0.8044 (ppp) REVERT: B 254 ASP cc_start: 0.8639 (t0) cc_final: 0.7996 (t0) REVERT: B 312 ASP cc_start: 0.9018 (t0) cc_final: 0.8603 (t0) REVERT: A 296 LEU cc_start: 0.9064 (mm) cc_final: 0.8675 (tt) REVERT: A 317 ARG cc_start: 0.8757 (mtm110) cc_final: 0.8238 (ptp90) REVERT: A 392 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8641 (mt-10) REVERT: G 14 LYS cc_start: 0.9167 (mmmm) cc_final: 0.8841 (mmpt) REVERT: G 20 LYS cc_start: 0.9009 (tppp) cc_final: 0.8727 (mtmp) REVERT: G 21 MET cc_start: 0.9049 (tpp) cc_final: 0.8593 (ttt) REVERT: G 58 GLU cc_start: 0.8719 (pm20) cc_final: 0.8455 (pm20) REVERT: S 73 ASP cc_start: 0.8487 (t70) cc_final: 0.7568 (t0) REVERT: S 76 LYS cc_start: 0.8890 (ptpp) cc_final: 0.8427 (ptpp) REVERT: S 234 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8663 (pt0) REVERT: N 73 ASP cc_start: 0.7745 (t70) cc_final: 0.7079 (t0) REVERT: N 83 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8772 (mtp) outliers start: 17 outliers final: 14 residues processed: 157 average time/residue: 1.4181 time to fit residues: 238.3010 Evaluate side-chains 161 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 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 N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 20 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.3310 r_free = 0.3310 target = 0.082011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.055591 restraints weight = 22708.521| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 3.35 r_work: 0.2583 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10107 Z= 0.203 Angle : 0.601 9.003 13703 Z= 0.306 Chirality : 0.042 0.142 1539 Planarity : 0.004 0.057 1748 Dihedral : 3.967 22.135 1387 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.41 % Allowed : 19.04 % Favored : 79.55 % 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: 2.02 (0.26), residues: 393 sheet: 0.96 (0.28), residues: 323 loop : -0.72 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 193 HIS 0.004 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 *********************** 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 159 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: R 85 ASP cc_start: 0.7982 (t70) cc_final: 0.7710 (t70) REVERT: R 100 LYS cc_start: 0.8664 (tppt) cc_final: 0.8100 (mttm) REVERT: R 136 ASP cc_start: 0.8770 (t0) cc_final: 0.8546 (t0) REVERT: R 311 MET cc_start: 0.8709 (mtp) cc_final: 0.8388 (mtm) REVERT: R 323 TRP cc_start: 0.8186 (m100) cc_final: 0.7812 (m-10) REVERT: B 10 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8878 (mm-30) REVERT: B 15 LYS cc_start: 0.8923 (mmmm) cc_final: 0.8686 (tptt) REVERT: B 25 CYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8012 (t) REVERT: B 59 TYR cc_start: 0.9216 (OUTLIER) cc_final: 0.8123 (m-80) REVERT: B 214 ARG cc_start: 0.9110 (mmm-85) cc_final: 0.8884 (mmm-85) REVERT: B 217 MET cc_start: 0.8615 (ptm) cc_final: 0.7934 (ppp) REVERT: B 254 ASP cc_start: 0.8548 (t0) cc_final: 0.7886 (t0) REVERT: B 312 ASP cc_start: 0.9018 (t0) cc_final: 0.8646 (t0) REVERT: A 296 LEU cc_start: 0.9039 (mm) cc_final: 0.8653 (tt) REVERT: A 317 ARG cc_start: 0.8778 (mtm110) cc_final: 0.8281 (ptp90) REVERT: A 365 CYS cc_start: 0.8241 (m) cc_final: 0.6882 (t) REVERT: A 392 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8621 (mt-10) REVERT: G 14 LYS cc_start: 0.9138 (mmmm) cc_final: 0.8811 (mmpt) REVERT: G 20 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8775 (mtmp) REVERT: G 21 MET cc_start: 0.9057 (tpp) cc_final: 0.8620 (ttt) REVERT: G 58 GLU cc_start: 0.8641 (pm20) cc_final: 0.8396 (pm20) REVERT: S 43 LYS cc_start: 0.9006 (mmtm) cc_final: 0.8789 (mmpt) REVERT: S 73 ASP cc_start: 0.8447 (t70) cc_final: 0.7548 (t0) REVERT: S 76 LYS cc_start: 0.8897 (ptpp) cc_final: 0.8442 (ptpp) REVERT: S 234 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8660 (pt0) REVERT: N 46 GLU cc_start: 0.8521 (pt0) cc_final: 0.8266 (pt0) REVERT: N 83 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8747 (mtp) outliers start: 15 outliers final: 9 residues processed: 153 average time/residue: 1.3676 time to fit residues: 223.6509 Evaluate side-chains 157 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 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 83 MET Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 35 optimal weight: 0.8980 chunk 96 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 ASN S 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.082048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.055528 restraints weight = 22563.769| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.33 r_work: 0.2596 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10107 Z= 0.201 Angle : 0.601 8.897 13703 Z= 0.305 Chirality : 0.042 0.144 1539 Planarity : 0.004 0.060 1748 Dihedral : 3.864 21.297 1387 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.51 % Allowed : 18.94 % Favored : 79.55 % 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: 0.98 (0.23), residues: 1245 helix: 2.07 (0.26), residues: 393 sheet: 1.00 (0.28), residues: 323 loop : -0.67 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 193 HIS 0.004 0.001 HIS A 357 PHE 0.010 0.001 PHE S 203 TYR 0.015 0.001 TYR S 190 ARG 0.015 0.000 ARG N 105 ********************** 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 160 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 1.132 Fit side-chains revert: symmetry clash REVERT: R 85 ASP cc_start: 0.7957 (t70) cc_final: 0.7663 (t70) REVERT: R 100 LYS cc_start: 0.8664 (tppt) cc_final: 0.8091 (mttm) REVERT: R 136 ASP cc_start: 0.8754 (t0) cc_final: 0.8544 (t0) REVERT: R 311 MET cc_start: 0.8728 (mtp) cc_final: 0.8444 (mtm) REVERT: R 323 TRP cc_start: 0.8199 (m100) cc_final: 0.7916 (m-10) REVERT: B 10 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8869 (mm-30) REVERT: B 15 LYS cc_start: 0.8928 (mmmm) cc_final: 0.8691 (tptt) REVERT: B 25 CYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8041 (t) REVERT: B 59 TYR cc_start: 0.9216 (OUTLIER) cc_final: 0.8179 (m-80) REVERT: B 214 ARG cc_start: 0.9124 (mmm-85) cc_final: 0.8881 (mmm-85) REVERT: B 217 MET cc_start: 0.8629 (ptm) cc_final: 0.7937 (ppp) REVERT: B 254 ASP cc_start: 0.8561 (t0) cc_final: 0.7924 (t0) REVERT: B 312 ASP cc_start: 0.9041 (t0) cc_final: 0.8658 (t0) REVERT: A 296 LEU cc_start: 0.9051 (mm) cc_final: 0.8661 (tt) REVERT: A 317 ARG cc_start: 0.8810 (mtm110) cc_final: 0.8360 (ptp90) REVERT: A 365 CYS cc_start: 0.8247 (m) cc_final: 0.6894 (t) REVERT: A 392 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8655 (mt-10) REVERT: G 13 ARG cc_start: 0.8888 (ttm110) cc_final: 0.8196 (ptp-110) REVERT: G 14 LYS cc_start: 0.9150 (mmmm) cc_final: 0.8795 (mmpt) REVERT: G 21 MET cc_start: 0.9057 (tpp) cc_final: 0.8616 (ttp) REVERT: G 58 GLU cc_start: 0.8622 (pm20) cc_final: 0.8386 (pm20) REVERT: S 43 LYS cc_start: 0.8996 (mmtm) cc_final: 0.8728 (mppt) REVERT: S 73 ASP cc_start: 0.8441 (t70) cc_final: 0.7523 (t0) REVERT: S 76 LYS cc_start: 0.8855 (ptpp) cc_final: 0.8409 (ptpp) REVERT: S 234 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8633 (pt0) REVERT: N 46 GLU cc_start: 0.8427 (pt0) cc_final: 0.8201 (pt0) REVERT: N 83 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8748 (mtp) outliers start: 16 outliers final: 9 residues processed: 152 average time/residue: 1.4119 time to fit residues: 228.9758 Evaluate side-chains 155 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 B residue 25 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 93 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3310 r_free = 0.3310 target = 0.081922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.055358 restraints weight = 22782.687| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.34 r_work: 0.2595 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10107 Z= 0.213 Angle : 0.618 10.716 13703 Z= 0.312 Chirality : 0.042 0.142 1539 Planarity : 0.004 0.061 1748 Dihedral : 3.901 21.593 1387 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.94 % Allowed : 19.98 % Favored : 79.08 % 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: 0.97 (0.23), residues: 1245 helix: 2.01 (0.26), residues: 394 sheet: 1.02 (0.28), residues: 323 loop : -0.67 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 193 HIS 0.004 0.001 HIS A 357 PHE 0.010 0.001 PHE S 203 TYR 0.015 0.001 TYR S 190 ARG 0.015 0.001 ARG N 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7521.56 seconds wall clock time: 133 minutes 13.97 seconds (7993.97 seconds total)