Starting phenix.real_space_refine on Sat Aug 23 02:53:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jiu_36328/08_2025/8jiu_36328.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jiu_36328/08_2025/8jiu_36328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jiu_36328/08_2025/8jiu_36328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jiu_36328/08_2025/8jiu_36328.map" model { file = "/net/cci-nas-00/data/ceres_data/8jiu_36328/08_2025/8jiu_36328.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jiu_36328/08_2025/8jiu_36328.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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 57 5.16 5 C 5767 2.51 5 N 1588 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9075 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1875 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "P" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Chain: "P" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 214 Classifications: {'peptide': 28} Modifications used: {'PEPT-D': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2548 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1, 'ARG:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 420 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 964 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3018 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 5, 'TRP:plan': 1, 'ASP:plan': 8, 'ASN:plan1': 2, 'HIS:plan': 4, 'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 127 Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'D6M': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D6M:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.24, per 1000 atoms: 0.25 Number of scatterers: 9075 At special positions: 0 Unit cell: (78.183, 100.674, 171.36, 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 57 16.00 O 1663 8.00 N 1588 7.00 C 5767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.05 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 67 " distance=2.01 Simple disulfide: pdb=" SG CYS R 58 " - pdb=" SG CYS R 100 " distance=2.04 Simple disulfide: pdb=" SG CYS R 81 " - pdb=" SG CYS R 121 " distance=2.04 Simple disulfide: pdb=" SG CYS R 224 " - pdb=" SG CYS R 294 " 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 Links applied TRANS " DSN P 2 " - " HIS P 1 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 367.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DSN P 2 " Number of C-beta restraints generated: 2204 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 41.0% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 9 through 38 removed outlier: 4.068A pdb=" N ARG A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.899A pdb=" N THR A 55 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 56 " --> pdb=" O LYS A 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 52 through 56' Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.584A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.697A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 297 Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.582A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.624A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.962A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'P' and resid 2 through 29 Processing helix chain 'B' and resid 3 through 25 removed outlier: 4.130A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.521A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 22 removed outlier: 3.662A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 46 removed outlier: 4.292A pdb=" N LYS C 46 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.624A pdb=" N GLU C 58 " --> pdb=" O PRO C 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.710A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.632A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.823A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 47 removed outlier: 3.614A pdb=" N GLU R 34 " --> pdb=" O ASP R 30 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS R 35 " --> pdb=" O PHE R 31 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N HIS R 44 " --> pdb=" O GLY R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 91 removed outlier: 4.312A pdb=" N HIS R 89 " --> pdb=" O PRO R 86 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS R 90 " --> pdb=" O TRP R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 164 removed outlier: 3.585A pdb=" N ILE R 128 " --> pdb=" O ASP R 124 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY R 148 " --> pdb=" O MET R 144 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA R 155 " --> pdb=" O LEU R 151 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 201 removed outlier: 3.784A pdb=" N ILE R 176 " --> pdb=" O THR R 172 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP R 195 " --> pdb=" O VAL R 191 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY R 196 " --> pdb=" O LEU R 192 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU R 197 " --> pdb=" O VAL R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 216 Processing helix chain 'R' and resid 220 through 252 removed outlier: 3.700A pdb=" N GLY R 234 " --> pdb=" O PHE R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 271 Processing helix chain 'R' and resid 272 through 289 removed outlier: 4.371A pdb=" N MET R 276 " --> pdb=" O TRP R 272 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU R 277 " --> pdb=" O GLY R 273 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE R 278 " --> pdb=" O ALA R 274 " (cutoff:3.500A) Proline residue: R 281 - end of helix Processing helix chain 'R' and resid 300 through 307 removed outlier: 4.355A pdb=" N ILE R 306 " --> pdb=" O PHE R 303 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 336 removed outlier: 4.077A pdb=" N ASN R 318 " --> pdb=" O ALA R 314 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE R 321 " --> pdb=" O ILE R 317 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA R 331 " --> pdb=" O GLN R 327 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG R 336 " --> pdb=" O LYS R 332 " (cutoff:3.500A) Processing helix chain 'R' and resid 343 through 353 removed outlier: 4.161A pdb=" N LEU R 347 " --> pdb=" O TYR R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 354 through 358 removed outlier: 4.055A pdb=" N LEU R 357 " --> pdb=" O LEU R 354 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU R 358 " --> pdb=" O ILE R 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 354 through 358' Processing helix chain 'R' and resid 360 through 365 Processing helix chain 'R' and resid 374 through 402 removed outlier: 3.545A pdb=" N ARG R 378 " --> pdb=" O GLN R 374 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER R 379 " --> pdb=" O GLY R 375 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LEU R 394 " --> pdb=" O SER R 390 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 417 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 3.564A pdb=" N THR A 210 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 50 removed outlier: 6.675A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.660A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.720A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.295A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.945A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.416A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.717A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.593A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.917A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1749 1.32 - 1.45: 2511 1.45 - 1.57: 4931 1.57 - 1.70: 2 1.70 - 1.82: 78 Bond restraints: 9271 Sorted by residual: bond pdb=" CA PHE R 365 " pdb=" C PHE R 365 " ideal model delta sigma weight residual 1.533 1.493 0.040 5.60e-03 3.19e+04 5.19e+01 bond pdb=" C07 D6M P 101 " pdb=" O08 D6M P 101 " ideal model delta sigma weight residual 1.247 1.371 -0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" C06 D6M P 101 " pdb=" C07 D6M P 101 " ideal model delta sigma weight residual 1.538 1.623 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" N ARG R 94 " pdb=" CA ARG R 94 " ideal model delta sigma weight residual 1.455 1.505 -0.050 1.23e-02 6.61e+03 1.64e+01 bond pdb=" CA THR N 111 " pdb=" C THR N 111 " ideal model delta sigma weight residual 1.523 1.475 0.047 1.28e-02 6.10e+03 1.37e+01 ... (remaining 9266 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.88: 12478 4.88 - 9.76: 94 9.76 - 14.63: 6 14.63 - 19.51: 1 19.51 - 24.39: 1 Bond angle restraints: 12580 Sorted by residual: angle pdb=" C06 D6M P 101 " pdb=" C07 D6M P 101 " pdb=" O08 D6M P 101 " ideal model delta sigma weight residual 118.04 93.65 24.39 3.00e+00 1.11e-01 6.61e+01 angle pdb=" N LEU B 30 " pdb=" CA LEU B 30 " pdb=" C LEU B 30 " ideal model delta sigma weight residual 113.43 104.11 9.32 1.26e+00 6.30e-01 5.47e+01 angle pdb=" N LEU R 47 " pdb=" CA LEU R 47 " pdb=" C LEU R 47 " ideal model delta sigma weight residual 112.23 102.92 9.31 1.26e+00 6.30e-01 5.46e+01 angle pdb=" N VAL R 280 " pdb=" CA VAL R 280 " pdb=" CB VAL R 280 " ideal model delta sigma weight residual 110.50 115.02 -4.52 6.30e-01 2.52e+00 5.15e+01 angle pdb=" N GLY R 196 " pdb=" CA GLY R 196 " pdb=" C GLY R 196 " ideal model delta sigma weight residual 112.50 104.46 8.04 1.16e+00 7.43e-01 4.81e+01 ... (remaining 12575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 4709 17.30 - 34.60: 473 34.60 - 51.90: 208 51.90 - 69.20: 67 69.20 - 86.50: 17 Dihedral angle restraints: 5474 sinusoidal: 2064 harmonic: 3410 Sorted by residual: dihedral pdb=" C VAL R 280 " pdb=" N VAL R 280 " pdb=" CA VAL R 280 " pdb=" CB VAL R 280 " ideal model delta harmonic sigma weight residual -122.00 -138.87 16.87 0 2.50e+00 1.60e-01 4.56e+01 dihedral pdb=" N VAL R 280 " pdb=" C VAL R 280 " pdb=" CA VAL R 280 " pdb=" CB VAL R 280 " ideal model delta harmonic sigma weight residual 123.40 138.75 -15.35 0 2.50e+00 1.60e-01 3.77e+01 dihedral pdb=" CB CYS R 43 " pdb=" SG CYS R 43 " pdb=" SG CYS R 67 " pdb=" CB CYS R 67 " ideal model delta sinusoidal sigma weight residual -86.00 -39.94 -46.06 1 1.00e+01 1.00e-02 2.94e+01 ... (remaining 5471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 1300 0.119 - 0.238: 93 0.238 - 0.357: 12 0.357 - 0.476: 3 0.476 - 0.595: 4 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA VAL R 280 " pdb=" N VAL R 280 " pdb=" C VAL R 280 " pdb=" CB VAL R 280 " both_signs ideal model delta sigma weight residual False 2.44 1.85 0.59 2.00e-01 2.50e+01 8.85e+00 chirality pdb=" CG LEU R 85 " pdb=" CB LEU R 85 " pdb=" CD1 LEU R 85 " pdb=" CD2 LEU R 85 " both_signs ideal model delta sigma weight residual False -2.59 -2.02 -0.57 2.00e-01 2.50e+01 8.16e+00 chirality pdb=" CA PHE B 292 " pdb=" N PHE B 292 " pdb=" C PHE B 292 " pdb=" CB PHE B 292 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.82e+00 ... (remaining 1409 not shown) Planarity restraints: 1610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 52 " -0.027 2.00e-02 2.50e+03 5.45e-02 2.97e+01 pdb=" C THR C 52 " 0.094 2.00e-02 2.50e+03 pdb=" O THR C 52 " -0.036 2.00e-02 2.50e+03 pdb=" N PRO C 53 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 D6M P 101 " 0.018 2.00e-02 2.50e+03 3.17e-02 1.26e+01 pdb=" C04 D6M P 101 " -0.038 2.00e-02 2.50e+03 pdb=" C12 D6M P 101 " -0.031 2.00e-02 2.50e+03 pdb=" N03 D6M P 101 " 0.047 2.00e-02 2.50e+03 pdb=" O01 D6M P 101 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA DSN P 2 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C DSN P 2 " -0.058 2.00e-02 2.50e+03 pdb=" O DSN P 2 " 0.022 2.00e-02 2.50e+03 pdb=" N GLN P 3 " 0.019 2.00e-02 2.50e+03 ... (remaining 1607 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1586 2.75 - 3.29: 8760 3.29 - 3.83: 15412 3.83 - 4.36: 17898 4.36 - 4.90: 30053 Nonbonded interactions: 73709 Sorted by model distance: nonbonded pdb=" N GLN R 120 " pdb=" OE1 GLN R 120 " model vdw 2.217 3.120 nonbonded pdb=" O SER R 203 " pdb=" OG SER R 203 " model vdw 2.254 3.040 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.265 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.311 3.040 nonbonded pdb=" O ASP B 228 " pdb=" OG SER B 245 " model vdw 2.318 3.040 ... (remaining 73704 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.810 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 : 0.008 0.214 9279 Z= 0.577 Angle : 1.143 24.390 12595 Z= 0.730 Chirality : 0.075 0.595 1412 Planarity : 0.006 0.080 1609 Dihedral : 18.355 86.500 3249 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 1.29 % Allowed : 6.38 % Favored : 92.33 % Rotamer: Outliers : 15.73 % Allowed : 7.54 % Favored : 76.72 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.62 (0.23), residues: 1160 helix: -1.51 (0.24), residues: 437 sheet: -1.35 (0.35), residues: 211 loop : -1.99 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 389 TYR 0.019 0.001 TYR R 145 PHE 0.024 0.002 PHE N 68 TRP 0.022 0.002 TRP R 241 HIS 0.007 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00758 ( 9271) covalent geometry : angle 1.13835 (12580) SS BOND : bond 0.01362 ( 6) SS BOND : angle 2.94895 ( 12) hydrogen bonds : bond 0.22069 ( 425) hydrogen bonds : angle 8.23310 ( 1209) Misc. bond : bond 0.21436 ( 1) link_TRANS : bond 0.05338 ( 1) link_TRANS : angle 3.59883 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 193 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8272 (mm-30) REVERT: A 294 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8002 (tm-30) REVERT: P 21 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8077 (t0) REVERT: P 25 TRP cc_start: 0.8655 (t60) cc_final: 0.7492 (t60) REVERT: B 10 GLU cc_start: 0.9285 (OUTLIER) cc_final: 0.9015 (mm-30) REVERT: B 17 GLN cc_start: 0.9256 (OUTLIER) cc_final: 0.8716 (tm-30) REVERT: B 251 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8557 (mtt90) REVERT: B 259 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8598 (tt0) REVERT: B 301 LYS cc_start: 0.8543 (mmmt) cc_final: 0.8034 (mmmm) REVERT: C 17 GLU cc_start: 0.9309 (tp30) cc_final: 0.7822 (tm-30) REVERT: C 21 MET cc_start: 0.9221 (mmp) cc_final: 0.8750 (mmm) REVERT: C 26 ASP cc_start: 0.8828 (OUTLIER) cc_final: 0.8431 (p0) REVERT: C 28 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8317 (pp) REVERT: C 32 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8231 (tppt) REVERT: N 18 LEU cc_start: 0.8435 (mt) cc_final: 0.8176 (mt) REVERT: N 28 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8395 (p) REVERT: N 73 ASP cc_start: 0.8249 (t70) cc_final: 0.7858 (t0) REVERT: R 28 VAL cc_start: 0.8687 (OUTLIER) cc_final: 0.8180 (m) REVERT: R 30 ASP cc_start: 0.9594 (OUTLIER) cc_final: 0.9266 (p0) REVERT: R 39 TYR cc_start: 0.8495 (t80) cc_final: 0.8203 (t80) REVERT: R 88 HIS cc_start: 0.7919 (t-90) cc_final: 0.7692 (t-90) REVERT: R 123 MET cc_start: 0.7428 (mmt) cc_final: 0.7004 (mmm) REVERT: R 144 MET cc_start: 0.9261 (tmm) cc_final: 0.8503 (tmm) REVERT: R 145 TYR cc_start: 0.8980 (OUTLIER) cc_final: 0.8013 (p90) REVERT: R 211 SER cc_start: 0.9306 (OUTLIER) cc_final: 0.8992 (p) REVERT: R 231 MET cc_start: 0.9036 (ttp) cc_final: 0.8581 (ttp) REVERT: R 251 ASN cc_start: 0.8744 (t0) cc_final: 0.8120 (t0) REVERT: R 287 CYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8812 (t) REVERT: R 368 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8559 (t) REVERT: R 385 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8251 (t0) REVERT: R 405 LYS cc_start: 0.9022 (mmpt) cc_final: 0.8616 (mmmt) outliers start: 146 outliers final: 21 residues processed: 287 average time/residue: 0.5507 time to fit residues: 168.0680 Evaluate side-chains 187 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 58 CYS Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 108 ARG Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 145 TYR Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 211 SER Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 265 SER Chi-restraints excluded: chain R residue 287 CYS Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain R residue 385 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN R 46 ASN ** R 318 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 = 0.3746 r_free = 0.3746 target = 0.108696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.071560 restraints weight = 18556.730| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.60 r_work: 0.2944 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9279 Z= 0.184 Angle : 0.702 9.606 12595 Z= 0.369 Chirality : 0.044 0.289 1412 Planarity : 0.005 0.070 1609 Dihedral : 9.772 101.710 1365 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.52 % Favored : 94.22 % Rotamer: Outliers : 4.74 % Allowed : 18.64 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.24), residues: 1160 helix: -0.09 (0.25), residues: 444 sheet: -0.91 (0.34), residues: 212 loop : -1.77 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 99 TYR 0.023 0.001 TYR R 145 PHE 0.011 0.002 PHE R 184 TRP 0.017 0.002 TRP R 418 HIS 0.007 0.001 HIS R 45 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 9271) covalent geometry : angle 0.70126 (12580) SS BOND : bond 0.00608 ( 6) SS BOND : angle 1.35667 ( 12) hydrogen bonds : bond 0.05002 ( 425) hydrogen bonds : angle 5.18609 ( 1209) Misc. bond : bond 0.00106 ( 1) link_TRANS : bond 0.00180 ( 1) link_TRANS : angle 0.85146 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8451 (mm-30) REVERT: A 255 MET cc_start: 0.1202 (mmp) cc_final: 0.0998 (mmp) REVERT: A 292 ASN cc_start: 0.8856 (t0) cc_final: 0.8597 (t0) REVERT: A 294 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7911 (tm-30) REVERT: A 358 TYR cc_start: 0.8003 (m-80) cc_final: 0.7755 (m-80) REVERT: P 13 GLN cc_start: 0.8488 (tp40) cc_final: 0.8233 (tp40) REVERT: P 24 GLU cc_start: 0.8999 (pp20) cc_final: 0.8596 (pp20) REVERT: B 17 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8668 (tm-30) REVERT: C 17 GLU cc_start: 0.9255 (tp30) cc_final: 0.9052 (mm-30) REVERT: C 21 MET cc_start: 0.8788 (mmp) cc_final: 0.8469 (mmm) REVERT: C 28 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8273 (pp) REVERT: C 32 LYS cc_start: 0.8948 (tptp) cc_final: 0.8342 (tppt) REVERT: C 38 MET cc_start: 0.8942 (mmm) cc_final: 0.8694 (mmm) REVERT: C 42 GLU cc_start: 0.8637 (pp20) cc_final: 0.8293 (pm20) REVERT: C 48 ASP cc_start: 0.8919 (t0) cc_final: 0.8545 (t0) REVERT: N 18 LEU cc_start: 0.8217 (mt) cc_final: 0.7933 (mt) REVERT: N 73 ASP cc_start: 0.8186 (t70) cc_final: 0.7549 (t0) REVERT: R 39 TYR cc_start: 0.8472 (t80) cc_final: 0.8091 (t80) REVERT: R 170 HIS cc_start: 0.6614 (OUTLIER) cc_final: 0.5531 (t70) REVERT: R 231 MET cc_start: 0.8681 (ttp) cc_final: 0.8383 (ttp) REVERT: R 405 LYS cc_start: 0.8847 (mmpt) cc_final: 0.8451 (mmmt) outliers start: 44 outliers final: 19 residues processed: 180 average time/residue: 0.5713 time to fit residues: 109.4168 Evaluate side-chains 165 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 108 ARG Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 170 HIS Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 344 LYS Chi-restraints excluded: chain R residue 358 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.7980 chunk 71 optimal weight: 0.0050 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 16 ASN N 120 GLN R 45 HIS ** R 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.108980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.071819 restraints weight = 18113.161| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.60 r_work: 0.2951 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9279 Z= 0.140 Angle : 0.634 11.547 12595 Z= 0.327 Chirality : 0.042 0.276 1412 Planarity : 0.005 0.067 1609 Dihedral : 7.675 83.543 1324 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.66 % Favored : 95.09 % Rotamer: Outliers : 3.77 % Allowed : 21.44 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.25), residues: 1160 helix: 0.46 (0.26), residues: 456 sheet: -0.64 (0.34), residues: 215 loop : -1.58 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 99 TYR 0.021 0.001 TYR R 145 PHE 0.011 0.001 PHE P 6 TRP 0.030 0.002 TRP R 115 HIS 0.010 0.002 HIS R 44 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9271) covalent geometry : angle 0.63304 (12580) SS BOND : bond 0.00451 ( 6) SS BOND : angle 1.46372 ( 12) hydrogen bonds : bond 0.04316 ( 425) hydrogen bonds : angle 4.63782 ( 1209) Misc. bond : bond 0.00013 ( 1) link_TRANS : bond 0.00098 ( 1) link_TRANS : angle 0.72619 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8444 (mm-30) REVERT: A 255 MET cc_start: 0.1006 (mmp) cc_final: 0.0781 (mmp) REVERT: A 292 ASN cc_start: 0.8856 (t0) cc_final: 0.8643 (t0) REVERT: A 294 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7892 (tm-30) REVERT: A 333 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8474 (tmm-80) REVERT: A 358 TYR cc_start: 0.7998 (m-80) cc_final: 0.7751 (m-80) REVERT: A 386 MET cc_start: 0.9113 (ttp) cc_final: 0.8889 (ttp) REVERT: P 13 GLN cc_start: 0.8471 (tp40) cc_final: 0.8182 (tp-100) REVERT: P 15 GLU cc_start: 0.8547 (tt0) cc_final: 0.8072 (tm-30) REVERT: P 24 GLU cc_start: 0.9035 (pp20) cc_final: 0.8817 (pp20) REVERT: B 12 GLU cc_start: 0.9286 (tm-30) cc_final: 0.9038 (pp20) REVERT: B 45 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.8813 (mtt) REVERT: B 301 LYS cc_start: 0.8447 (mmmm) cc_final: 0.8083 (mmmm) REVERT: C 21 MET cc_start: 0.8762 (mmp) cc_final: 0.8447 (mmm) REVERT: C 28 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8198 (pp) REVERT: C 32 LYS cc_start: 0.8944 (tptp) cc_final: 0.8370 (tppt) REVERT: C 42 GLU cc_start: 0.8675 (pp20) cc_final: 0.8292 (pm20) REVERT: C 44 HIS cc_start: 0.6617 (p90) cc_final: 0.6315 (p-80) REVERT: C 48 ASP cc_start: 0.8857 (t0) cc_final: 0.8330 (t0) REVERT: N 68 PHE cc_start: 0.7693 (m-10) cc_final: 0.7410 (m-10) REVERT: N 73 ASP cc_start: 0.8240 (t70) cc_final: 0.7515 (t0) REVERT: N 123 GLN cc_start: 0.8156 (tp-100) cc_final: 0.7940 (tp-100) REVERT: R 31 PHE cc_start: 0.9398 (m-80) cc_final: 0.9152 (m-80) REVERT: R 39 TYR cc_start: 0.8847 (t80) cc_final: 0.8447 (t80) REVERT: R 115 TRP cc_start: 0.7641 (p-90) cc_final: 0.7181 (p-90) REVERT: R 127 GLU cc_start: 0.8740 (pm20) cc_final: 0.8429 (mm-30) REVERT: R 170 HIS cc_start: 0.6575 (OUTLIER) cc_final: 0.5435 (t70) REVERT: R 231 MET cc_start: 0.8652 (ttp) cc_final: 0.8342 (ttp) REVERT: R 260 GLU cc_start: 0.8607 (pt0) cc_final: 0.8157 (pm20) REVERT: R 405 LYS cc_start: 0.8886 (mmpt) cc_final: 0.8491 (mmmt) REVERT: R 410 GLU cc_start: 0.8245 (tm-30) cc_final: 0.8028 (tm-30) outliers start: 35 outliers final: 13 residues processed: 165 average time/residue: 0.5658 time to fit residues: 99.3366 Evaluate side-chains 161 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 170 HIS Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 364 VAL Chi-restraints excluded: chain R residue 420 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 17 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 44 HIS ** R 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.107466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.070009 restraints weight = 18582.884| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.64 r_work: 0.2910 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 9279 Z= 0.169 Angle : 0.652 13.685 12595 Z= 0.336 Chirality : 0.043 0.260 1412 Planarity : 0.004 0.059 1609 Dihedral : 6.673 77.187 1310 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.31 % Favored : 95.43 % Rotamer: Outliers : 3.66 % Allowed : 22.74 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.25), residues: 1160 helix: 0.77 (0.26), residues: 457 sheet: -0.60 (0.33), residues: 216 loop : -1.47 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 317 TYR 0.021 0.001 TYR R 145 PHE 0.013 0.001 PHE N 108 TRP 0.017 0.001 TRP R 115 HIS 0.015 0.002 HIS R 44 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 9271) covalent geometry : angle 0.65054 (12580) SS BOND : bond 0.00359 ( 6) SS BOND : angle 1.66293 ( 12) hydrogen bonds : bond 0.04196 ( 425) hydrogen bonds : angle 4.40623 ( 1209) Misc. bond : bond 0.00017 ( 1) link_TRANS : bond 0.00060 ( 1) link_TRANS : angle 0.69723 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.1083 (mmp) cc_final: 0.0821 (mmp) REVERT: A 294 GLN cc_start: 0.8411 (tm-30) cc_final: 0.7998 (tm-30) REVERT: A 333 ARG cc_start: 0.8734 (ptp90) cc_final: 0.8428 (tmm-80) REVERT: A 358 TYR cc_start: 0.7985 (m-80) cc_final: 0.7700 (m-80) REVERT: P 13 GLN cc_start: 0.8445 (tp40) cc_final: 0.7896 (tp-100) REVERT: P 15 GLU cc_start: 0.8613 (tt0) cc_final: 0.8153 (tm-30) REVERT: P 24 GLU cc_start: 0.9026 (pp20) cc_final: 0.8778 (pp20) REVERT: B 9 GLN cc_start: 0.9575 (mp10) cc_final: 0.9341 (mp10) REVERT: B 12 GLU cc_start: 0.9262 (tm-30) cc_final: 0.8984 (pp20) REVERT: C 17 GLU cc_start: 0.9348 (mm-30) cc_final: 0.9127 (mm-30) REVERT: C 28 ILE cc_start: 0.8763 (mm) cc_final: 0.8170 (pp) REVERT: C 48 ASP cc_start: 0.8913 (t0) cc_final: 0.8332 (t0) REVERT: N 73 ASP cc_start: 0.8213 (t70) cc_final: 0.7511 (t0) REVERT: N 123 GLN cc_start: 0.8249 (tp-100) cc_final: 0.7962 (tp-100) REVERT: R 39 TYR cc_start: 0.8843 (t80) cc_final: 0.8415 (t80) REVERT: R 115 TRP cc_start: 0.7733 (p-90) cc_final: 0.7124 (p-90) REVERT: R 127 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8571 (pm20) REVERT: R 385 ASP cc_start: 0.8990 (OUTLIER) cc_final: 0.8747 (m-30) outliers start: 34 outliers final: 17 residues processed: 166 average time/residue: 0.5781 time to fit residues: 102.3039 Evaluate side-chains 158 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 127 GLU Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 344 LYS Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 364 VAL Chi-restraints excluded: chain R residue 385 ASP Chi-restraints excluded: chain R residue 420 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 42 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 84 optimal weight: 20.0000 chunk 14 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 177 HIS ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.105789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.068488 restraints weight = 18399.013| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.59 r_work: 0.2877 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 9279 Z= 0.198 Angle : 0.677 14.113 12595 Z= 0.345 Chirality : 0.043 0.229 1412 Planarity : 0.005 0.059 1609 Dihedral : 6.186 57.201 1304 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.40 % Favored : 95.34 % Rotamer: Outliers : 4.20 % Allowed : 24.57 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.25), residues: 1160 helix: 0.76 (0.26), residues: 463 sheet: -0.40 (0.33), residues: 215 loop : -1.44 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 317 TYR 0.022 0.002 TYR R 145 PHE 0.014 0.001 PHE N 108 TRP 0.015 0.002 TRP P 25 HIS 0.020 0.002 HIS R 44 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 9271) covalent geometry : angle 0.67493 (12580) SS BOND : bond 0.00316 ( 6) SS BOND : angle 1.77804 ( 12) hydrogen bonds : bond 0.04143 ( 425) hydrogen bonds : angle 4.32414 ( 1209) Misc. bond : bond 0.00011 ( 1) link_TRANS : bond 0.00014 ( 1) link_TRANS : angle 0.69146 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8570 (mm-30) REVERT: A 228 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8035 (mtp85) REVERT: A 255 MET cc_start: 0.1161 (mmp) cc_final: 0.0880 (mmp) REVERT: A 292 ASN cc_start: 0.8920 (t0) cc_final: 0.8665 (t0) REVERT: A 294 GLN cc_start: 0.8436 (tm-30) cc_final: 0.7969 (tm-30) REVERT: A 333 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8486 (tmm-80) REVERT: A 358 TYR cc_start: 0.8022 (m-80) cc_final: 0.7713 (m-80) REVERT: P 13 GLN cc_start: 0.8453 (tp40) cc_final: 0.7895 (tp-100) REVERT: P 15 GLU cc_start: 0.8640 (tt0) cc_final: 0.8115 (tm-30) REVERT: P 24 GLU cc_start: 0.9027 (pp20) cc_final: 0.8743 (pp20) REVERT: B 9 GLN cc_start: 0.9578 (mp10) cc_final: 0.9337 (mp10) REVERT: B 12 GLU cc_start: 0.9230 (tm-30) cc_final: 0.8967 (pp20) REVERT: B 301 LYS cc_start: 0.8493 (mmmm) cc_final: 0.8264 (mmmm) REVERT: C 17 GLU cc_start: 0.9299 (mm-30) cc_final: 0.9080 (mm-30) REVERT: C 26 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.8375 (t0) REVERT: C 28 ILE cc_start: 0.8796 (mm) cc_final: 0.8562 (pp) REVERT: C 47 GLU cc_start: 0.8018 (pp20) cc_final: 0.7725 (pp20) REVERT: C 48 ASP cc_start: 0.8957 (t0) cc_final: 0.8450 (t0) REVERT: N 73 ASP cc_start: 0.8202 (t70) cc_final: 0.7532 (t0) REVERT: N 123 GLN cc_start: 0.8333 (tp-100) cc_final: 0.7976 (tp-100) REVERT: R 39 TYR cc_start: 0.9071 (t80) cc_final: 0.8576 (t80) REVERT: R 170 HIS cc_start: 0.6665 (OUTLIER) cc_final: 0.5500 (t70) REVERT: R 385 ASP cc_start: 0.8992 (OUTLIER) cc_final: 0.8753 (m-30) outliers start: 39 outliers final: 20 residues processed: 167 average time/residue: 0.5935 time to fit residues: 105.4257 Evaluate side-chains 164 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 170 HIS Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 344 LYS Chi-restraints excluded: chain R residue 355 ILE Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 364 VAL Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain R residue 385 ASP Chi-restraints excluded: chain R residue 386 LEU Chi-restraints excluded: chain R residue 420 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.104724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.069052 restraints weight = 18573.591| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.45 r_work: 0.2868 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 9279 Z= 0.221 Angle : 0.711 14.587 12595 Z= 0.360 Chirality : 0.044 0.221 1412 Planarity : 0.005 0.058 1609 Dihedral : 6.217 58.083 1304 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.57 % Favored : 95.17 % Rotamer: Outliers : 3.99 % Allowed : 26.08 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.25), residues: 1160 helix: 0.86 (0.26), residues: 458 sheet: -0.25 (0.33), residues: 218 loop : -1.41 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 105 TYR 0.023 0.002 TYR R 145 PHE 0.015 0.001 PHE N 108 TRP 0.041 0.002 TRP R 115 HIS 0.008 0.001 HIS R 88 Details of bonding type rmsd covalent geometry : bond 0.00520 ( 9271) covalent geometry : angle 0.70867 (12580) SS BOND : bond 0.00276 ( 6) SS BOND : angle 1.85460 ( 12) hydrogen bonds : bond 0.04207 ( 425) hydrogen bonds : angle 4.32151 ( 1209) Misc. bond : bond 0.00001 ( 1) link_TRANS : bond 0.00021 ( 1) link_TRANS : angle 0.67661 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8157 (mtp85) REVERT: A 292 ASN cc_start: 0.9032 (t0) cc_final: 0.8790 (t0) REVERT: A 294 GLN cc_start: 0.8445 (tm-30) cc_final: 0.7988 (tm-30) REVERT: A 333 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8481 (tmm-80) REVERT: A 358 TYR cc_start: 0.7998 (m-80) cc_final: 0.7697 (m-80) REVERT: P 13 GLN cc_start: 0.8516 (tp40) cc_final: 0.7973 (tp-100) REVERT: P 15 GLU cc_start: 0.8735 (tt0) cc_final: 0.8223 (tm-30) REVERT: P 24 GLU cc_start: 0.9055 (pp20) cc_final: 0.8783 (pp20) REVERT: B 9 GLN cc_start: 0.9590 (mp10) cc_final: 0.9326 (mp10) REVERT: B 12 GLU cc_start: 0.9191 (tm-30) cc_final: 0.8906 (pp20) REVERT: B 45 MET cc_start: 0.9355 (mtt) cc_final: 0.8799 (mtt) REVERT: B 301 LYS cc_start: 0.8728 (mmmm) cc_final: 0.8488 (mmmm) REVERT: C 13 ARG cc_start: 0.9118 (tmm160) cc_final: 0.8673 (tmm160) REVERT: C 17 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8893 (mm-30) REVERT: C 26 ASP cc_start: 0.8675 (m-30) cc_final: 0.8420 (t0) REVERT: C 48 ASP cc_start: 0.8948 (t0) cc_final: 0.8355 (t0) REVERT: N 73 ASP cc_start: 0.8332 (t70) cc_final: 0.7628 (t0) REVERT: N 123 GLN cc_start: 0.8492 (tp-100) cc_final: 0.8131 (tp-100) REVERT: R 31 PHE cc_start: 0.9640 (m-80) cc_final: 0.9129 (m-10) REVERT: R 39 TYR cc_start: 0.9082 (t80) cc_final: 0.8487 (t80) REVERT: R 43 CYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8537 (p) REVERT: R 115 TRP cc_start: 0.7852 (p-90) cc_final: 0.7141 (p-90) REVERT: R 328 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8611 (tp) REVERT: R 385 ASP cc_start: 0.9067 (OUTLIER) cc_final: 0.8843 (m-30) outliers start: 37 outliers final: 23 residues processed: 170 average time/residue: 0.5659 time to fit residues: 102.6834 Evaluate side-chains 167 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 43 CYS Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 328 LEU Chi-restraints excluded: chain R residue 344 LYS Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 364 VAL Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain R residue 385 ASP Chi-restraints excluded: chain R residue 386 LEU Chi-restraints excluded: chain R residue 420 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 27 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 30.0000 chunk 109 optimal weight: 6.9990 chunk 82 optimal weight: 30.0000 chunk 94 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.105211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.069247 restraints weight = 18679.950| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.47 r_work: 0.2872 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9279 Z= 0.198 Angle : 0.718 13.905 12595 Z= 0.364 Chirality : 0.043 0.217 1412 Planarity : 0.005 0.055 1609 Dihedral : 5.968 58.774 1302 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.40 % Favored : 95.34 % Rotamer: Outliers : 3.99 % Allowed : 27.16 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.25), residues: 1160 helix: 0.98 (0.26), residues: 459 sheet: -0.06 (0.33), residues: 213 loop : -1.38 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 105 TYR 0.022 0.001 TYR R 145 PHE 0.013 0.001 PHE P 6 TRP 0.028 0.002 TRP R 115 HIS 0.005 0.001 HIS R 45 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 9271) covalent geometry : angle 0.71675 (12580) SS BOND : bond 0.00257 ( 6) SS BOND : angle 1.74467 ( 12) hydrogen bonds : bond 0.04116 ( 425) hydrogen bonds : angle 4.28240 ( 1209) Misc. bond : bond 0.00011 ( 1) link_TRANS : bond 0.00009 ( 1) link_TRANS : angle 0.69775 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8682 (mm-30) REVERT: A 228 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8181 (mtp85) REVERT: A 292 ASN cc_start: 0.8990 (t0) cc_final: 0.8777 (t0) REVERT: A 294 GLN cc_start: 0.8401 (tm-30) cc_final: 0.7940 (tm-30) REVERT: A 333 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8479 (tmm-80) REVERT: A 358 TYR cc_start: 0.8004 (m-80) cc_final: 0.7694 (m-80) REVERT: P 13 GLN cc_start: 0.8490 (tp40) cc_final: 0.7959 (tp-100) REVERT: P 15 GLU cc_start: 0.8758 (tt0) cc_final: 0.8223 (tm-30) REVERT: P 24 GLU cc_start: 0.9096 (pp20) cc_final: 0.8810 (pp20) REVERT: B 9 GLN cc_start: 0.9618 (mp10) cc_final: 0.9363 (mp10) REVERT: B 12 GLU cc_start: 0.9168 (tm-30) cc_final: 0.8871 (pp20) REVERT: B 45 MET cc_start: 0.9352 (mtt) cc_final: 0.8744 (mtt) REVERT: B 301 LYS cc_start: 0.8755 (mmmm) cc_final: 0.8506 (mmmm) REVERT: C 13 ARG cc_start: 0.9095 (tmm160) cc_final: 0.8795 (tmm160) REVERT: C 17 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8741 (mm-30) REVERT: C 48 ASP cc_start: 0.8903 (t0) cc_final: 0.7561 (t0) REVERT: N 73 ASP cc_start: 0.8353 (t70) cc_final: 0.7646 (t0) REVERT: N 123 GLN cc_start: 0.8541 (tp-100) cc_final: 0.8224 (tp-100) REVERT: R 30 ASP cc_start: 0.9656 (p0) cc_final: 0.9327 (p0) REVERT: R 31 PHE cc_start: 0.9662 (OUTLIER) cc_final: 0.9159 (m-10) REVERT: R 39 TYR cc_start: 0.9084 (t80) cc_final: 0.8479 (t80) REVERT: R 115 TRP cc_start: 0.8047 (p-90) cc_final: 0.7195 (p-90) REVERT: R 170 HIS cc_start: 0.6684 (OUTLIER) cc_final: 0.5477 (t70) outliers start: 37 outliers final: 23 residues processed: 167 average time/residue: 0.6055 time to fit residues: 107.7696 Evaluate side-chains 167 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 31 PHE Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 170 HIS Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 344 LYS Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain R residue 386 LEU Chi-restraints excluded: chain R residue 420 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 76 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 108 optimal weight: 0.0040 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.106088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.069480 restraints weight = 18500.840| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.51 r_work: 0.2897 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 9279 Z= 0.162 Angle : 0.722 13.914 12595 Z= 0.363 Chirality : 0.043 0.213 1412 Planarity : 0.005 0.062 1609 Dihedral : 5.881 58.899 1302 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.48 % Favored : 95.26 % Rotamer: Outliers : 3.66 % Allowed : 27.69 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.25), residues: 1160 helix: 1.13 (0.26), residues: 457 sheet: 0.10 (0.34), residues: 209 loop : -1.32 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 105 TYR 0.020 0.001 TYR R 145 PHE 0.012 0.001 PHE P 6 TRP 0.025 0.002 TRP R 115 HIS 0.008 0.001 HIS R 45 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9271) covalent geometry : angle 0.72018 (12580) SS BOND : bond 0.00207 ( 6) SS BOND : angle 1.65154 ( 12) hydrogen bonds : bond 0.03923 ( 425) hydrogen bonds : angle 4.17353 ( 1209) Misc. bond : bond 0.00023 ( 1) link_TRANS : bond 0.00069 ( 1) link_TRANS : angle 0.70704 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8599 (mm-30) REVERT: A 292 ASN cc_start: 0.8990 (t0) cc_final: 0.8763 (t0) REVERT: A 294 GLN cc_start: 0.8370 (tm-30) cc_final: 0.7911 (tm-30) REVERT: A 333 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8447 (tmm-80) REVERT: A 358 TYR cc_start: 0.8002 (m-80) cc_final: 0.7704 (m-80) REVERT: P 13 GLN cc_start: 0.8450 (tp40) cc_final: 0.7953 (tp-100) REVERT: P 15 GLU cc_start: 0.8713 (tt0) cc_final: 0.8151 (tm-30) REVERT: P 24 GLU cc_start: 0.9078 (pp20) cc_final: 0.8814 (pp20) REVERT: B 9 GLN cc_start: 0.9612 (mp10) cc_final: 0.9394 (mp10) REVERT: B 12 GLU cc_start: 0.9170 (tm-30) cc_final: 0.8863 (pp20) REVERT: B 45 MET cc_start: 0.9372 (mtt) cc_final: 0.8785 (mtt) REVERT: B 301 LYS cc_start: 0.8761 (mmmm) cc_final: 0.8534 (mmmm) REVERT: C 13 ARG cc_start: 0.9104 (tmm160) cc_final: 0.8896 (tmm160) REVERT: C 17 GLU cc_start: 0.9251 (mm-30) cc_final: 0.8868 (mm-30) REVERT: C 21 MET cc_start: 0.8871 (mmp) cc_final: 0.8638 (mmm) REVERT: C 48 ASP cc_start: 0.8492 (t0) cc_final: 0.8287 (t0) REVERT: N 73 ASP cc_start: 0.8336 (t70) cc_final: 0.7653 (t0) REVERT: N 123 GLN cc_start: 0.8487 (tp-100) cc_final: 0.8086 (tp-100) REVERT: R 30 ASP cc_start: 0.9556 (p0) cc_final: 0.9303 (p0) REVERT: R 31 PHE cc_start: 0.9648 (m-80) cc_final: 0.9174 (m-10) REVERT: R 39 TYR cc_start: 0.9079 (t80) cc_final: 0.8568 (t80) REVERT: R 317 ILE cc_start: 0.7985 (tp) cc_final: 0.7639 (pt) outliers start: 34 outliers final: 21 residues processed: 170 average time/residue: 0.5325 time to fit residues: 96.8638 Evaluate side-chains 161 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 344 LYS Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 364 VAL Chi-restraints excluded: chain R residue 420 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 16 optimal weight: 0.0060 chunk 72 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN R 45 HIS ** R 318 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 = 0.3732 r_free = 0.3732 target = 0.107767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.071217 restraints weight = 18535.499| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.53 r_work: 0.2928 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9279 Z= 0.138 Angle : 0.735 12.352 12595 Z= 0.369 Chirality : 0.043 0.246 1412 Planarity : 0.005 0.059 1609 Dihedral : 5.723 58.169 1302 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.88 % Favored : 95.78 % Rotamer: Outliers : 2.05 % Allowed : 30.06 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.25), residues: 1160 helix: 1.26 (0.26), residues: 449 sheet: 0.21 (0.34), residues: 209 loop : -1.29 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 105 TYR 0.019 0.001 TYR R 145 PHE 0.015 0.001 PHE P 22 TRP 0.048 0.002 TRP R 115 HIS 0.025 0.001 HIS R 45 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9271) covalent geometry : angle 0.73325 (12580) SS BOND : bond 0.00333 ( 6) SS BOND : angle 1.60590 ( 12) hydrogen bonds : bond 0.03737 ( 425) hydrogen bonds : angle 4.11357 ( 1209) Misc. bond : bond 0.00021 ( 1) link_TRANS : bond 0.00127 ( 1) link_TRANS : angle 0.73083 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8669 (mm-30) REVERT: A 292 ASN cc_start: 0.9018 (t0) cc_final: 0.8771 (t0) REVERT: A 294 GLN cc_start: 0.8305 (tm-30) cc_final: 0.7824 (tm-30) REVERT: A 297 LEU cc_start: 0.9097 (mm) cc_final: 0.8842 (mm) REVERT: A 333 ARG cc_start: 0.8690 (ptp90) cc_final: 0.8440 (tmm-80) REVERT: A 358 TYR cc_start: 0.7976 (m-80) cc_final: 0.7698 (m-80) REVERT: P 13 GLN cc_start: 0.8400 (tp40) cc_final: 0.7935 (tp-100) REVERT: P 15 GLU cc_start: 0.8772 (tt0) cc_final: 0.8162 (tm-30) REVERT: P 21 ASP cc_start: 0.9201 (t0) cc_final: 0.8713 (t0) REVERT: P 24 GLU cc_start: 0.9043 (pp20) cc_final: 0.8784 (pp20) REVERT: B 9 GLN cc_start: 0.9605 (mp10) cc_final: 0.9370 (mp10) REVERT: B 12 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8848 (pp20) REVERT: B 260 GLU cc_start: 0.8836 (pt0) cc_final: 0.8008 (tt0) REVERT: B 262 MET cc_start: 0.8384 (tpp) cc_final: 0.8117 (tpp) REVERT: C 13 ARG cc_start: 0.9058 (tmm160) cc_final: 0.8849 (tmm160) REVERT: C 17 GLU cc_start: 0.9269 (mm-30) cc_final: 0.8899 (mm-30) REVERT: C 20 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8774 (pmtt) REVERT: C 21 MET cc_start: 0.8824 (mmp) cc_final: 0.8478 (mmm) REVERT: C 46 LYS cc_start: 0.8957 (ttpp) cc_final: 0.8574 (pptt) REVERT: C 48 ASP cc_start: 0.8753 (t0) cc_final: 0.7918 (t0) REVERT: N 73 ASP cc_start: 0.8369 (t70) cc_final: 0.7739 (t0) REVERT: N 123 GLN cc_start: 0.8700 (tp-100) cc_final: 0.8295 (tp-100) REVERT: R 30 ASP cc_start: 0.9511 (p0) cc_final: 0.9194 (p0) REVERT: R 31 PHE cc_start: 0.9657 (OUTLIER) cc_final: 0.9202 (m-10) REVERT: R 39 TYR cc_start: 0.9117 (t80) cc_final: 0.8637 (t80) REVERT: R 65 TYR cc_start: 0.8085 (p90) cc_final: 0.7813 (p90) REVERT: R 115 TRP cc_start: 0.7727 (p-90) cc_final: 0.7178 (p-90) REVERT: R 317 ILE cc_start: 0.7897 (tp) cc_final: 0.7587 (pt) outliers start: 19 outliers final: 15 residues processed: 161 average time/residue: 0.5734 time to fit residues: 98.5428 Evaluate side-chains 160 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 31 PHE Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 344 LYS Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 364 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 62 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 51 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.108444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.072122 restraints weight = 18523.948| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.55 r_work: 0.2943 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9279 Z= 0.136 Angle : 0.734 12.699 12595 Z= 0.368 Chirality : 0.042 0.228 1412 Planarity : 0.005 0.063 1609 Dihedral : 5.599 57.794 1302 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.31 % Favored : 95.34 % Rotamer: Outliers : 1.72 % Allowed : 30.17 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.25), residues: 1160 helix: 1.31 (0.26), residues: 449 sheet: 0.29 (0.35), residues: 207 loop : -1.26 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 105 TYR 0.016 0.001 TYR R 145 PHE 0.011 0.001 PHE P 6 TRP 0.033 0.002 TRP R 115 HIS 0.011 0.001 HIS R 45 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9271) covalent geometry : angle 0.73343 (12580) SS BOND : bond 0.00288 ( 6) SS BOND : angle 1.45240 ( 12) hydrogen bonds : bond 0.03632 ( 425) hydrogen bonds : angle 4.00958 ( 1209) Misc. bond : bond 0.00022 ( 1) link_TRANS : bond 0.00162 ( 1) link_TRANS : angle 0.72984 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8656 (mm-30) REVERT: A 292 ASN cc_start: 0.9001 (t0) cc_final: 0.8759 (t0) REVERT: A 294 GLN cc_start: 0.8320 (tm-30) cc_final: 0.7905 (tm-30) REVERT: A 333 ARG cc_start: 0.8677 (ptp90) cc_final: 0.8442 (tmm-80) REVERT: A 358 TYR cc_start: 0.7923 (m-80) cc_final: 0.7593 (m-80) REVERT: P 13 GLN cc_start: 0.8381 (tp40) cc_final: 0.7932 (tp-100) REVERT: P 15 GLU cc_start: 0.8699 (tt0) cc_final: 0.8056 (tm-30) REVERT: P 24 GLU cc_start: 0.9059 (pp20) cc_final: 0.8761 (pp20) REVERT: B 9 GLN cc_start: 0.9597 (mp10) cc_final: 0.9374 (mp10) REVERT: B 12 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8818 (pp20) REVERT: B 260 GLU cc_start: 0.8851 (pt0) cc_final: 0.8017 (tt0) REVERT: B 262 MET cc_start: 0.8360 (tpp) cc_final: 0.7962 (tpp) REVERT: C 17 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8956 (mm-30) REVERT: C 20 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8752 (pmtt) REVERT: C 21 MET cc_start: 0.8807 (mmp) cc_final: 0.8536 (mmm) REVERT: C 48 ASP cc_start: 0.8692 (t0) cc_final: 0.7386 (t0) REVERT: N 38 ARG cc_start: 0.9209 (ptt180) cc_final: 0.8787 (ptt-90) REVERT: N 73 ASP cc_start: 0.8360 (t70) cc_final: 0.7742 (t0) REVERT: R 30 ASP cc_start: 0.9436 (p0) cc_final: 0.9108 (p0) REVERT: R 31 PHE cc_start: 0.9633 (m-80) cc_final: 0.9196 (m-10) REVERT: R 39 TYR cc_start: 0.9137 (t80) cc_final: 0.8632 (t80) REVERT: R 63 ASP cc_start: 0.8764 (t0) cc_final: 0.7826 (m-30) REVERT: R 115 TRP cc_start: 0.7741 (p-90) cc_final: 0.7016 (p-90) REVERT: R 317 ILE cc_start: 0.7821 (tp) cc_final: 0.7524 (pt) outliers start: 16 outliers final: 11 residues processed: 158 average time/residue: 0.5203 time to fit residues: 87.9179 Evaluate side-chains 156 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 364 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 54 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN C 24 ASN ** R 318 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 = 0.3733 r_free = 0.3733 target = 0.107734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.071001 restraints weight = 18408.637| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.53 r_work: 0.2924 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9279 Z= 0.151 Angle : 0.747 14.518 12595 Z= 0.371 Chirality : 0.042 0.206 1412 Planarity : 0.005 0.064 1609 Dihedral : 5.608 58.016 1302 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.79 % Favored : 95.86 % Rotamer: Outliers : 1.72 % Allowed : 30.71 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.25), residues: 1160 helix: 1.14 (0.26), residues: 458 sheet: 0.31 (0.35), residues: 207 loop : -1.25 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 105 TYR 0.018 0.001 TYR R 145 PHE 0.019 0.001 PHE P 22 TRP 0.033 0.002 TRP R 115 HIS 0.006 0.001 HIS R 45 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9271) covalent geometry : angle 0.74560 (12580) SS BOND : bond 0.00269 ( 6) SS BOND : angle 1.55158 ( 12) hydrogen bonds : bond 0.03694 ( 425) hydrogen bonds : angle 4.05046 ( 1209) Misc. bond : bond 0.00025 ( 1) link_TRANS : bond 0.00119 ( 1) link_TRANS : angle 0.68745 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3567.91 seconds wall clock time: 61 minutes 26.18 seconds (3686.18 seconds total)