Starting phenix.real_space_refine on Thu Mar 13 22:05:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jiu_36328/03_2025/8jiu_36328.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jiu_36328/03_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_36328/03_2025/8jiu_36328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jiu_36328/03_2025/8jiu_36328.map" model { file = "/net/cci-nas-00/data/ceres_data/8jiu_36328/03_2025/8jiu_36328.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jiu_36328/03_2025/8jiu_36328.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 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: {'GLN:plan1': 1, 'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 5} 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: 5.73, per 1000 atoms: 0.63 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: 2.36 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.92 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: 3.04 Time building geometry restraints manager: 2.83 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: 0.010 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.290 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:18.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.280 ------------------------------------------------------------------------------- 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 0.124 9271 Z= 0.482 Angle : 1.138 24.390 12580 Z= 0.729 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.022 0.002 TRP R 241 HIS 0.007 0.001 HIS B 91 PHE 0.024 0.002 PHE N 68 TYR 0.019 0.001 TYR R 145 ARG 0.008 0.000 ARG A 389 *********************** 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 : 1.190 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: 0.8074 (t0) REVERT: P 25 TRP cc_start: 0.8655 (t60) cc_final: 0.7569 (t60) REVERT: B 10 GLU cc_start: 0.9285 (OUTLIER) cc_final: 0.9017 (mm-30) REVERT: B 17 GLN cc_start: 0.9256 (OUTLIER) cc_final: 0.8708 (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: 0.8584 (tm-30) REVERT: C 21 MET cc_start: 0.9221 (mmp) cc_final: 0.9009 (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: 0.8242 (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: 0.8095 (m) REVERT: R 30 ASP cc_start: 0.9594 (OUTLIER) cc_final: 0.9256 (p0) REVERT: R 39 TYR cc_start: 0.8495 (t80) cc_final: 0.8155 (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: 0.7005 (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 201 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7789 (ttt90) REVERT: R 211 SER cc_start: 0.9306 (OUTLIER) cc_final: 0.8993 (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: 0.8813 (t) REVERT: R 293 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7776 (mm-40) REVERT: R 368 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8560 (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: 1.2375 time to fit residues: 378.8933 Evaluate side-chains 189 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 201 ARG 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 293 GLN 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 96 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 89 optimal weight: 0.0870 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.110495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.073876 restraints weight = 18284.882| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.58 r_work: 0.2992 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9271 Z= 0.212 Angle : 0.680 9.427 12580 Z= 0.358 Chirality : 0.043 0.308 1412 Planarity : 0.005 0.069 1609 Dihedral : 10.005 100.187 1372 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.78 % Favored : 93.97 % Rotamer: Outliers : 4.42 % Allowed : 19.18 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.24), residues: 1160 helix: -0.06 (0.25), residues: 444 sheet: -0.96 (0.34), residues: 214 loop : -1.76 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 418 HIS 0.005 0.001 HIS R 45 PHE 0.011 0.001 PHE R 33 TYR 0.023 0.001 TYR R 145 ARG 0.013 0.001 ARG C 27 *********************** 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 196 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8464 (mm-30) REVERT: A 255 MET cc_start: 0.1251 (mmp) cc_final: 0.1036 (mmp) REVERT: A 292 ASN cc_start: 0.8799 (t0) cc_final: 0.8548 (t0) REVERT: A 294 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7887 (tm-30) REVERT: P 13 GLN cc_start: 0.8470 (tp40) cc_final: 0.8159 (tp-100) REVERT: P 24 GLU cc_start: 0.8907 (pp20) cc_final: 0.8380 (pp20) REVERT: P 26 LEU cc_start: 0.9468 (tp) cc_final: 0.8946 (tp) REVERT: B 13 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8979 (mm110) REVERT: B 17 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8627 (tm-30) REVERT: C 17 GLU cc_start: 0.9282 (tp30) cc_final: 0.8442 (tp30) REVERT: C 21 MET cc_start: 0.8714 (mmp) cc_final: 0.8335 (mmm) REVERT: C 28 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8293 (pp) REVERT: C 32 LYS cc_start: 0.8915 (tptp) cc_final: 0.8241 (tppt) REVERT: C 42 GLU cc_start: 0.8763 (pp20) cc_final: 0.8413 (pm20) REVERT: C 48 ASP cc_start: 0.8867 (t0) cc_final: 0.8622 (t0) REVERT: N 18 LEU cc_start: 0.8175 (mt) cc_final: 0.7954 (mt) REVERT: N 73 ASP cc_start: 0.8209 (t70) cc_final: 0.7638 (t0) REVERT: R 36 TRP cc_start: 0.9325 (OUTLIER) cc_final: 0.9081 (t-100) REVERT: R 39 TYR cc_start: 0.8398 (t80) cc_final: 0.8009 (t80) REVERT: R 170 HIS cc_start: 0.6359 (OUTLIER) cc_final: 0.5270 (t70) REVERT: R 231 MET cc_start: 0.8721 (ttp) cc_final: 0.8398 (ttp) REVERT: R 245 GLU cc_start: 0.9058 (tp30) cc_final: 0.8856 (mm-30) REVERT: R 405 LYS cc_start: 0.8833 (mmpt) cc_final: 0.8435 (mmmt) outliers start: 41 outliers final: 16 residues processed: 181 average time/residue: 1.3146 time to fit residues: 254.5672 Evaluate side-chains 165 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLN 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 B residue 338 ILE 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 N residue 111 THR Chi-restraints excluded: chain R residue 36 TRP 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 60 optimal weight: 9.9990 chunk 73 optimal weight: 0.6980 chunk 55 optimal weight: 0.1980 chunk 13 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 77 optimal weight: 50.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.109416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.072410 restraints weight = 18356.518| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.59 r_work: 0.2959 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9271 Z= 0.219 Angle : 0.635 9.942 12580 Z= 0.330 Chirality : 0.042 0.300 1412 Planarity : 0.005 0.073 1609 Dihedral : 7.602 82.771 1324 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.40 % Favored : 95.34 % Rotamer: Outliers : 3.56 % Allowed : 21.34 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.25), residues: 1160 helix: 0.58 (0.26), residues: 444 sheet: -0.66 (0.34), residues: 216 loop : -1.60 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP R 115 HIS 0.010 0.002 HIS R 44 PHE 0.010 0.001 PHE P 6 TYR 0.021 0.001 TYR R 145 ARG 0.008 0.001 ARG R 99 *********************** 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 181 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.931 Fit side-chains REVERT: A 27 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8453 (mm-30) REVERT: A 255 MET cc_start: 0.1275 (mmp) cc_final: 0.1025 (mmp) REVERT: A 292 ASN cc_start: 0.8830 (t0) cc_final: 0.8598 (t0) REVERT: A 294 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7927 (tm-30) REVERT: A 333 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8446 (tmm-80) REVERT: A 358 TYR cc_start: 0.8004 (m-80) cc_final: 0.7791 (m-80) REVERT: P 13 GLN cc_start: 0.8437 (tp40) cc_final: 0.8145 (tp-100) REVERT: P 15 GLU cc_start: 0.8660 (tt0) cc_final: 0.8200 (tm-30) REVERT: P 24 GLU cc_start: 0.8972 (pp20) cc_final: 0.8759 (pp20) REVERT: B 9 GLN cc_start: 0.9607 (mp10) cc_final: 0.9277 (mp10) REVERT: B 10 GLU cc_start: 0.9566 (tp30) cc_final: 0.9365 (tp30) REVERT: B 12 GLU cc_start: 0.9287 (tm-30) cc_final: 0.8815 (pp20) REVERT: B 13 GLN cc_start: 0.9317 (OUTLIER) cc_final: 0.8563 (mm-40) REVERT: B 45 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8752 (mtt) REVERT: B 301 LYS cc_start: 0.8323 (mmmt) cc_final: 0.8061 (mmmm) REVERT: C 17 GLU cc_start: 0.9234 (tp30) cc_final: 0.8563 (tp30) REVERT: C 21 MET cc_start: 0.8790 (mmp) cc_final: 0.8457 (mmm) REVERT: C 28 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8238 (pp) REVERT: C 32 LYS cc_start: 0.8944 (tptp) cc_final: 0.8332 (tppt) REVERT: C 42 GLU cc_start: 0.8683 (pp20) cc_final: 0.8304 (pm20) REVERT: C 48 ASP cc_start: 0.8876 (t0) cc_final: 0.8354 (t0) REVERT: N 73 ASP cc_start: 0.8211 (t70) cc_final: 0.7484 (t0) REVERT: N 123 GLN cc_start: 0.7999 (tp-100) cc_final: 0.7790 (tp-100) REVERT: R 29 MET cc_start: 0.8941 (tpp) cc_final: 0.8739 (tpp) REVERT: R 31 PHE cc_start: 0.9411 (m-80) cc_final: 0.9073 (m-80) REVERT: R 39 TYR cc_start: 0.8787 (t80) cc_final: 0.8300 (t80) REVERT: R 115 TRP cc_start: 0.7538 (p-90) cc_final: 0.7315 (p-90) REVERT: R 127 GLU cc_start: 0.8934 (mp0) cc_final: 0.8696 (mp0) REVERT: R 170 HIS cc_start: 0.6513 (OUTLIER) cc_final: 0.5434 (t70) REVERT: R 231 MET cc_start: 0.8688 (ttp) cc_final: 0.8439 (ttp) REVERT: R 260 GLU cc_start: 0.8596 (pt0) cc_final: 0.8080 (pm20) REVERT: R 405 LYS cc_start: 0.8876 (mmpt) cc_final: 0.8476 (mmmt) outliers start: 33 outliers final: 13 residues processed: 165 average time/residue: 1.2512 time to fit residues: 220.5479 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 : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 333 ARG 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 B residue 338 ILE Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 57 SER 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 200 THR Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 368 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 113 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 108 optimal weight: 0.4980 chunk 44 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.108507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.071241 restraints weight = 18297.202| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.60 r_work: 0.2934 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9271 Z= 0.232 Angle : 0.627 10.070 12580 Z= 0.326 Chirality : 0.042 0.277 1412 Planarity : 0.004 0.059 1609 Dihedral : 6.572 78.191 1311 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.48 % Favored : 95.26 % Rotamer: Outliers : 3.12 % Allowed : 22.84 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.25), residues: 1160 helix: 0.85 (0.26), residues: 455 sheet: -0.54 (0.33), residues: 216 loop : -1.50 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 115 HIS 0.015 0.001 HIS R 44 PHE 0.016 0.001 PHE R 33 TYR 0.020 0.001 TYR R 145 ARG 0.007 0.000 ARG A 317 *********************** 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: 29 poor density : 152 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.1103 (mmp) cc_final: 0.0840 (mmp) REVERT: A 292 ASN cc_start: 0.8882 (t0) cc_final: 0.8669 (t0) REVERT: A 294 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7996 (tm-30) REVERT: A 333 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8420 (tmm-80) REVERT: A 358 TYR cc_start: 0.7999 (m-80) cc_final: 0.7764 (m-80) REVERT: P 13 GLN cc_start: 0.8433 (tp40) cc_final: 0.8084 (tm-30) REVERT: P 21 ASP cc_start: 0.9125 (t0) cc_final: 0.8675 (t0) REVERT: P 24 GLU cc_start: 0.8958 (pp20) cc_final: 0.8697 (pp20) REVERT: B 9 GLN cc_start: 0.9627 (mp10) cc_final: 0.9422 (mp10) REVERT: B 12 GLU cc_start: 0.9296 (tm-30) cc_final: 0.9079 (pp20) REVERT: B 45 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8741 (mtt) REVERT: B 301 LYS cc_start: 0.8463 (mmmt) cc_final: 0.8104 (mmmm) REVERT: C 17 GLU cc_start: 0.9233 (tp30) cc_final: 0.8642 (tp30) REVERT: C 21 MET cc_start: 0.8744 (mmp) cc_final: 0.8544 (mmp) REVERT: C 28 ILE cc_start: 0.8756 (mm) cc_final: 0.8143 (pp) REVERT: C 32 LYS cc_start: 0.8926 (tptp) cc_final: 0.8301 (tppt) REVERT: C 42 GLU cc_start: 0.8710 (pp20) cc_final: 0.8423 (pm20) REVERT: C 48 ASP cc_start: 0.8935 (t0) cc_final: 0.8463 (t0) REVERT: N 73 ASP cc_start: 0.8220 (t70) cc_final: 0.7526 (t0) REVERT: N 123 GLN cc_start: 0.8173 (tp-100) cc_final: 0.7900 (tp-100) REVERT: R 39 TYR cc_start: 0.8761 (t80) cc_final: 0.8260 (t80) REVERT: R 65 TYR cc_start: 0.7614 (p90) cc_final: 0.7202 (p90) REVERT: R 115 TRP cc_start: 0.7663 (p-90) cc_final: 0.7183 (p-90) REVERT: R 123 MET cc_start: 0.6308 (mmt) cc_final: 0.6009 (mmp) REVERT: R 127 GLU cc_start: 0.8944 (mp0) cc_final: 0.8719 (mp0) REVERT: R 136 LYS cc_start: 0.8967 (mtpt) cc_final: 0.8735 (mtpp) REVERT: R 170 HIS cc_start: 0.6574 (OUTLIER) cc_final: 0.5519 (t70) REVERT: R 245 GLU cc_start: 0.8947 (tp30) cc_final: 0.8690 (tp30) REVERT: R 260 GLU cc_start: 0.8606 (pt0) cc_final: 0.8132 (pm20) outliers start: 29 outliers final: 16 residues processed: 166 average time/residue: 1.2516 time to fit residues: 221.6275 Evaluate side-chains 163 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 333 ARG 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 26 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 36 TRP 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 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 Chi-restraints excluded: chain R residue 386 LEU 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 108 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3743 r_free = 0.3743 target = 0.108657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.071522 restraints weight = 18204.858| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.59 r_work: 0.2938 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9271 Z= 0.211 Angle : 0.627 9.231 12580 Z= 0.323 Chirality : 0.042 0.253 1412 Planarity : 0.004 0.057 1609 Dihedral : 6.180 69.179 1307 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.57 % Favored : 95.17 % Rotamer: Outliers : 3.34 % Allowed : 24.89 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.25), residues: 1160 helix: 1.02 (0.26), residues: 456 sheet: -0.47 (0.33), residues: 217 loop : -1.42 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 215 HIS 0.021 0.001 HIS R 44 PHE 0.010 0.001 PHE P 6 TYR 0.020 0.001 TYR R 145 ARG 0.010 0.000 ARG N 105 *********************** 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 186 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8613 (mm-30) REVERT: A 255 MET cc_start: 0.1026 (mmp) cc_final: 0.0764 (mmp) REVERT: A 294 GLN cc_start: 0.8359 (tm-30) cc_final: 0.7951 (tm-30) REVERT: A 333 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8482 (tmm-80) REVERT: A 358 TYR cc_start: 0.7983 (m-80) cc_final: 0.7731 (m-80) REVERT: P 13 GLN cc_start: 0.8392 (tp40) cc_final: 0.7921 (tp-100) REVERT: P 15 GLU cc_start: 0.8705 (tt0) cc_final: 0.8176 (tm-30) REVERT: P 24 GLU cc_start: 0.9066 (pp20) cc_final: 0.8818 (pp20) REVERT: B 9 GLN cc_start: 0.9629 (mp10) cc_final: 0.9382 (mp10) REVERT: B 12 GLU cc_start: 0.9319 (tm-30) cc_final: 0.9092 (pp20) REVERT: B 45 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8927 (mtm) REVERT: C 17 GLU cc_start: 0.9233 (tp30) cc_final: 0.8583 (tp30) REVERT: C 26 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8383 (t0) REVERT: C 28 ILE cc_start: 0.8810 (mm) cc_final: 0.8576 (pp) REVERT: C 42 GLU cc_start: 0.8724 (pp20) cc_final: 0.8465 (pm20) REVERT: C 47 GLU cc_start: 0.7963 (pp20) cc_final: 0.7659 (pp20) REVERT: C 48 ASP cc_start: 0.8862 (t0) cc_final: 0.8304 (t0) REVERT: N 73 ASP cc_start: 0.8304 (t70) cc_final: 0.7620 (t0) REVERT: N 123 GLN cc_start: 0.8211 (tp-100) cc_final: 0.7888 (tp-100) REVERT: R 31 PHE cc_start: 0.9730 (OUTLIER) cc_final: 0.9432 (m-80) REVERT: R 39 TYR cc_start: 0.8972 (t80) cc_final: 0.8545 (t80) REVERT: R 65 TYR cc_start: 0.7478 (p90) cc_final: 0.7242 (p90) REVERT: R 115 TRP cc_start: 0.7665 (p-90) cc_final: 0.7171 (p-90) REVERT: R 136 LYS cc_start: 0.9011 (mtpt) cc_final: 0.8761 (mtpp) REVERT: R 170 HIS cc_start: 0.6668 (OUTLIER) cc_final: 0.5535 (t70) REVERT: R 260 GLU cc_start: 0.8589 (pt0) cc_final: 0.8130 (pm20) REVERT: R 385 ASP cc_start: 0.8982 (OUTLIER) cc_final: 0.8747 (m-30) outliers start: 31 outliers final: 11 residues processed: 171 average time/residue: 1.3504 time to fit residues: 246.1782 Evaluate side-chains 161 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 26 ASP Chi-restraints excluded: chain C residue 57 SER 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 170 HIS Chi-restraints excluded: chain R residue 191 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 93 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 67 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN N 31 ASN R 177 HIS ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.109029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.071880 restraints weight = 18155.417| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.61 r_work: 0.2938 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9271 Z= 0.193 Angle : 0.640 10.618 12580 Z= 0.325 Chirality : 0.041 0.227 1412 Planarity : 0.004 0.055 1609 Dihedral : 5.703 57.367 1304 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.31 % Favored : 95.43 % Rotamer: Outliers : 3.34 % Allowed : 26.29 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.25), residues: 1160 helix: 1.05 (0.26), residues: 463 sheet: -0.35 (0.33), residues: 215 loop : -1.41 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 215 HIS 0.008 0.001 HIS R 88 PHE 0.010 0.001 PHE P 6 TYR 0.020 0.001 TYR R 145 ARG 0.010 0.000 ARG N 105 *********************** 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 191 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8578 (mm-30) REVERT: A 255 MET cc_start: 0.1339 (mmp) cc_final: 0.1076 (mmp) REVERT: A 292 ASN cc_start: 0.8828 (t0) cc_final: 0.8576 (t0) REVERT: A 294 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7838 (tm-30) REVERT: A 333 ARG cc_start: 0.8720 (ptp90) cc_final: 0.8469 (tmm-80) REVERT: A 358 TYR cc_start: 0.7981 (m-80) cc_final: 0.7729 (m-80) REVERT: A 386 MET cc_start: 0.9128 (ttp) cc_final: 0.8926 (ttp) REVERT: P 13 GLN cc_start: 0.8348 (tp40) cc_final: 0.8047 (tp-100) REVERT: P 15 GLU cc_start: 0.8706 (tt0) cc_final: 0.8245 (tm-30) REVERT: P 24 GLU cc_start: 0.9077 (pp20) cc_final: 0.8822 (pp20) REVERT: B 9 GLN cc_start: 0.9655 (mp10) cc_final: 0.9401 (mp10) REVERT: B 12 GLU cc_start: 0.9321 (tm-30) cc_final: 0.9072 (pp20) REVERT: B 45 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8738 (mtt) REVERT: C 17 GLU cc_start: 0.9210 (tp30) cc_final: 0.8530 (tp30) REVERT: C 26 ASP cc_start: 0.8588 (m-30) cc_final: 0.8384 (t0) REVERT: C 48 ASP cc_start: 0.8821 (t0) cc_final: 0.8198 (t0) REVERT: N 68 PHE cc_start: 0.7803 (m-10) cc_final: 0.7586 (m-10) REVERT: N 73 ASP cc_start: 0.8310 (t70) cc_final: 0.7637 (t0) REVERT: N 123 GLN cc_start: 0.8252 (tp-100) cc_final: 0.7799 (tp-100) REVERT: R 39 TYR cc_start: 0.9028 (t80) cc_final: 0.8533 (t80) REVERT: R 115 TRP cc_start: 0.7676 (p-90) cc_final: 0.7143 (p-90) REVERT: R 123 MET cc_start: 0.6112 (OUTLIER) cc_final: 0.5876 (mmp) REVERT: R 127 GLU cc_start: 0.8886 (mp0) cc_final: 0.8648 (mp0) REVERT: R 136 LYS cc_start: 0.9028 (mtpt) cc_final: 0.8773 (mtpp) REVERT: R 405 LYS cc_start: 0.8958 (mmtt) cc_final: 0.8644 (mmpt) outliers start: 31 outliers final: 12 residues processed: 175 average time/residue: 1.2058 time to fit residues: 225.3399 Evaluate side-chains 162 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 16 SER 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 61 MET Chi-restraints excluded: chain B residue 93 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 62 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 82 optimal weight: 30.0000 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.108326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.070817 restraints weight = 18409.760| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.62 r_work: 0.2922 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9271 Z= 0.234 Angle : 0.691 13.383 12580 Z= 0.347 Chirality : 0.042 0.213 1412 Planarity : 0.005 0.054 1609 Dihedral : 5.744 57.810 1302 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.31 % Favored : 95.43 % Rotamer: Outliers : 3.02 % Allowed : 27.91 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.25), residues: 1160 helix: 1.03 (0.26), residues: 464 sheet: -0.27 (0.33), residues: 222 loop : -1.40 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 215 HIS 0.006 0.001 HIS R 88 PHE 0.011 0.001 PHE R 95 TYR 0.035 0.001 TYR R 65 ARG 0.012 0.001 ARG N 105 *********************** 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 181 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8565 (mm-30) REVERT: A 292 ASN cc_start: 0.8899 (t0) cc_final: 0.8666 (t0) REVERT: A 294 GLN cc_start: 0.8241 (tm-30) cc_final: 0.7862 (tm-30) REVERT: A 333 ARG cc_start: 0.8730 (ptp90) cc_final: 0.8439 (tmm-80) REVERT: A 358 TYR cc_start: 0.7965 (m-80) cc_final: 0.7696 (m-80) REVERT: A 386 MET cc_start: 0.9143 (ttp) cc_final: 0.8931 (ttp) REVERT: P 13 GLN cc_start: 0.8495 (tp40) cc_final: 0.8040 (tp-100) REVERT: P 15 GLU cc_start: 0.8730 (tt0) cc_final: 0.8206 (tm-30) REVERT: P 21 ASP cc_start: 0.9102 (OUTLIER) cc_final: 0.8522 (t0) REVERT: P 24 GLU cc_start: 0.9056 (pp20) cc_final: 0.8760 (pp20) REVERT: B 9 GLN cc_start: 0.9659 (mp10) cc_final: 0.9392 (mp10) REVERT: B 12 GLU cc_start: 0.9334 (tm-30) cc_final: 0.9062 (pp20) REVERT: B 45 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8973 (mtm) REVERT: C 17 GLU cc_start: 0.9295 (tp30) cc_final: 0.9074 (mm-30) REVERT: C 20 LYS cc_start: 0.8792 (ptpt) cc_final: 0.8310 (ptpt) REVERT: C 42 GLU cc_start: 0.8795 (pp20) cc_final: 0.8528 (pm20) REVERT: C 47 GLU cc_start: 0.7973 (pp20) cc_final: 0.7657 (pp20) REVERT: C 48 ASP cc_start: 0.8837 (t0) cc_final: 0.8144 (t0) REVERT: N 73 ASP cc_start: 0.8310 (t70) cc_final: 0.7649 (t0) REVERT: N 123 GLN cc_start: 0.8489 (tp-100) cc_final: 0.8074 (tp-100) REVERT: R 30 ASP cc_start: 0.9631 (p0) cc_final: 0.9303 (p0) REVERT: R 31 PHE cc_start: 0.9593 (OUTLIER) cc_final: 0.9223 (m-10) REVERT: R 39 TYR cc_start: 0.9133 (t80) cc_final: 0.8613 (t80) REVERT: R 65 TYR cc_start: 0.7956 (p90) cc_final: 0.7195 (p90) REVERT: R 88 HIS cc_start: 0.8950 (t-90) cc_final: 0.8540 (t-90) REVERT: R 136 LYS cc_start: 0.9039 (mtpt) cc_final: 0.8797 (mtpp) REVERT: R 170 HIS cc_start: 0.6592 (OUTLIER) cc_final: 0.5429 (t70) REVERT: R 328 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8357 (tp) outliers start: 28 outliers final: 17 residues processed: 169 average time/residue: 1.1861 time to fit residues: 214.2224 Evaluate side-chains 169 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain P residue 21 ASP 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 B residue 135 VAL Chi-restraints excluded: chain C residue 26 ASP 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 170 HIS 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 355 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 109 optimal weight: 6.9990 chunk 13 optimal weight: 0.0980 chunk 39 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 75 optimal weight: 0.0170 chunk 29 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.108845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.071402 restraints weight = 18490.532| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.63 r_work: 0.2933 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9271 Z= 0.218 Angle : 0.705 11.678 12580 Z= 0.355 Chirality : 0.043 0.286 1412 Planarity : 0.005 0.056 1609 Dihedral : 5.789 59.849 1302 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.05 % Favored : 95.69 % Rotamer: Outliers : 2.80 % Allowed : 28.56 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.25), residues: 1160 helix: 1.02 (0.26), residues: 466 sheet: -0.16 (0.34), residues: 215 loop : -1.35 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP R 115 HIS 0.009 0.001 HIS R 45 PHE 0.011 0.001 PHE P 6 TYR 0.033 0.001 TYR R 65 ARG 0.013 0.001 ARG N 105 *********************** 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 180 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8604 (mm-30) REVERT: A 292 ASN cc_start: 0.8867 (t0) cc_final: 0.8634 (t0) REVERT: A 294 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7835 (tm-30) REVERT: A 333 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8402 (tmm-80) REVERT: A 358 TYR cc_start: 0.7950 (m-80) cc_final: 0.7663 (m-80) REVERT: A 386 MET cc_start: 0.9159 (ttp) cc_final: 0.8936 (ttp) REVERT: P 13 GLN cc_start: 0.8465 (tp40) cc_final: 0.8041 (tp-100) REVERT: P 15 GLU cc_start: 0.8705 (tt0) cc_final: 0.8163 (tm-30) REVERT: P 24 GLU cc_start: 0.8996 (pp20) cc_final: 0.8664 (pp20) REVERT: B 9 GLN cc_start: 0.9672 (mp10) cc_final: 0.9426 (mm-40) REVERT: B 12 GLU cc_start: 0.9329 (tm-30) cc_final: 0.9035 (pp20) REVERT: B 45 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8936 (mtm) REVERT: C 20 LYS cc_start: 0.8714 (ptpt) cc_final: 0.8169 (ptpp) REVERT: C 42 GLU cc_start: 0.8816 (pp20) cc_final: 0.8533 (pm20) REVERT: C 48 ASP cc_start: 0.8828 (t0) cc_final: 0.8150 (t0) REVERT: N 73 ASP cc_start: 0.8292 (t70) cc_final: 0.7690 (t0) REVERT: N 123 GLN cc_start: 0.8497 (tp-100) cc_final: 0.8079 (tp-100) REVERT: R 30 ASP cc_start: 0.9586 (p0) cc_final: 0.9172 (p0) REVERT: R 31 PHE cc_start: 0.9587 (OUTLIER) cc_final: 0.9200 (m-10) REVERT: R 39 TYR cc_start: 0.9100 (t80) cc_final: 0.8632 (t80) REVERT: R 65 TYR cc_start: 0.7633 (p90) cc_final: 0.7030 (p90) REVERT: R 115 TRP cc_start: 0.8024 (p-90) cc_final: 0.7604 (p-90) REVERT: R 136 LYS cc_start: 0.9045 (mtpt) cc_final: 0.8802 (mtpp) outliers start: 26 outliers final: 17 residues processed: 169 average time/residue: 1.1819 time to fit residues: 213.7669 Evaluate side-chains 164 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 P residue 16 SER 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 61 MET Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 8 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 52 optimal weight: 0.0470 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3740 r_free = 0.3740 target = 0.108922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.071544 restraints weight = 18309.722| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.63 r_work: 0.2929 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9271 Z= 0.211 Angle : 0.716 11.343 12580 Z= 0.359 Chirality : 0.042 0.201 1412 Planarity : 0.005 0.059 1609 Dihedral : 5.742 59.215 1302 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.05 % Favored : 95.60 % Rotamer: Outliers : 2.59 % Allowed : 29.20 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.25), residues: 1160 helix: 1.06 (0.26), residues: 466 sheet: -0.10 (0.34), residues: 213 loop : -1.27 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP R 115 HIS 0.028 0.001 HIS R 45 PHE 0.010 0.001 PHE P 6 TYR 0.024 0.001 TYR R 65 ARG 0.014 0.001 ARG N 105 *********************** 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 170 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8541 (mm-30) REVERT: A 292 ASN cc_start: 0.8879 (t0) cc_final: 0.8653 (t0) REVERT: A 294 GLN cc_start: 0.8200 (tm-30) cc_final: 0.7798 (tm-30) REVERT: A 333 ARG cc_start: 0.8722 (ptp90) cc_final: 0.8393 (tmm-80) REVERT: A 358 TYR cc_start: 0.7958 (m-80) cc_final: 0.7676 (m-80) REVERT: A 386 MET cc_start: 0.9148 (ttp) cc_final: 0.8923 (ttp) REVERT: P 13 GLN cc_start: 0.8478 (tp40) cc_final: 0.8070 (tp-100) REVERT: P 24 GLU cc_start: 0.9001 (pp20) cc_final: 0.8650 (pp20) REVERT: P 27 LYS cc_start: 0.9111 (mptt) cc_final: 0.8843 (tppt) REVERT: B 9 GLN cc_start: 0.9667 (mp10) cc_final: 0.9416 (mm-40) REVERT: B 12 GLU cc_start: 0.9340 (tm-30) cc_final: 0.9029 (pp20) REVERT: B 45 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8911 (mtm) REVERT: B 260 GLU cc_start: 0.8854 (pt0) cc_final: 0.8157 (tt0) REVERT: C 42 GLU cc_start: 0.8869 (pp20) cc_final: 0.8609 (pm20) REVERT: C 48 ASP cc_start: 0.8746 (t0) cc_final: 0.7198 (t0) REVERT: N 73 ASP cc_start: 0.8286 (t70) cc_final: 0.7627 (t0) REVERT: N 123 GLN cc_start: 0.8474 (tp-100) cc_final: 0.8106 (tp-100) REVERT: R 31 PHE cc_start: 0.9560 (m-10) cc_final: 0.9226 (m-10) REVERT: R 39 TYR cc_start: 0.9181 (t80) cc_final: 0.8763 (t80) REVERT: R 63 ASP cc_start: 0.8765 (t0) cc_final: 0.7956 (m-30) REVERT: R 65 TYR cc_start: 0.7908 (p90) cc_final: 0.7332 (p90) REVERT: R 95 PHE cc_start: 0.8836 (m-10) cc_final: 0.8493 (m-80) REVERT: R 115 TRP cc_start: 0.8041 (p-90) cc_final: 0.7065 (p-90) REVERT: R 117 ASP cc_start: 0.8296 (p0) cc_final: 0.8083 (p0) REVERT: R 136 LYS cc_start: 0.9051 (mtpt) cc_final: 0.8812 (mtpp) REVERT: R 170 HIS cc_start: 0.6569 (OUTLIER) cc_final: 0.5397 (t70) outliers start: 24 outliers final: 15 residues processed: 160 average time/residue: 1.3365 time to fit residues: 227.8412 Evaluate side-chains 159 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL 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 45 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL 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 170 HIS Chi-restraints excluded: chain R residue 189 SER 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 84 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 88 optimal weight: 0.0570 chunk 90 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 80 optimal weight: 0.0050 chunk 87 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 overall best weight: 0.5914 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.109195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.072138 restraints weight = 18577.510| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.64 r_work: 0.2940 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9271 Z= 0.202 Angle : 0.719 12.534 12580 Z= 0.358 Chirality : 0.041 0.199 1412 Planarity : 0.005 0.062 1609 Dihedral : 5.462 58.281 1302 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.97 % Favored : 95.69 % Rotamer: Outliers : 2.16 % Allowed : 28.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.25), residues: 1160 helix: 1.14 (0.26), residues: 466 sheet: -0.10 (0.34), residues: 213 loop : -1.22 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 115 HIS 0.011 0.001 HIS R 45 PHE 0.021 0.001 PHE R 402 TYR 0.024 0.001 TYR R 65 ARG 0.014 0.001 ARG N 105 ********************** 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 169 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8472 (mm-30) REVERT: A 292 ASN cc_start: 0.8872 (t0) cc_final: 0.8642 (t0) REVERT: A 294 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7789 (tm-30) REVERT: A 333 ARG cc_start: 0.8729 (ptp90) cc_final: 0.8472 (tmm-80) REVERT: A 358 TYR cc_start: 0.7951 (m-80) cc_final: 0.7658 (m-80) REVERT: P 13 GLN cc_start: 0.8448 (tp40) cc_final: 0.8061 (tp-100) REVERT: P 15 GLU cc_start: 0.8742 (tt0) cc_final: 0.8286 (tm-30) REVERT: P 21 ASP cc_start: 0.9098 (t0) cc_final: 0.8532 (t0) REVERT: P 24 GLU cc_start: 0.8907 (pp20) cc_final: 0.8607 (pp20) REVERT: B 9 GLN cc_start: 0.9667 (mp10) cc_final: 0.9416 (mm-40) REVERT: B 12 GLU cc_start: 0.9330 (tm-30) cc_final: 0.9014 (pp20) REVERT: B 45 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8883 (mtt) REVERT: B 260 GLU cc_start: 0.8843 (pt0) cc_final: 0.8160 (tt0) REVERT: C 42 GLU cc_start: 0.8804 (pp20) cc_final: 0.8548 (pm20) REVERT: N 73 ASP cc_start: 0.8281 (t70) cc_final: 0.7431 (t0) REVERT: N 123 GLN cc_start: 0.8449 (tp-100) cc_final: 0.8086 (tp-100) REVERT: R 31 PHE cc_start: 0.9569 (m-10) cc_final: 0.9226 (m-10) REVERT: R 39 TYR cc_start: 0.9144 (t80) cc_final: 0.8770 (t80) REVERT: R 63 ASP cc_start: 0.8796 (t0) cc_final: 0.7977 (m-30) REVERT: R 65 TYR cc_start: 0.8031 (p90) cc_final: 0.7357 (p90) REVERT: R 95 PHE cc_start: 0.8752 (m-10) cc_final: 0.8398 (m-80) REVERT: R 115 TRP cc_start: 0.7911 (p-90) cc_final: 0.6980 (p-90) REVERT: R 117 ASP cc_start: 0.8287 (p0) cc_final: 0.8075 (p0) REVERT: R 136 LYS cc_start: 0.9065 (mtpt) cc_final: 0.8832 (mtpp) REVERT: R 317 ILE cc_start: 0.7692 (tp) cc_final: 0.7411 (pt) outliers start: 20 outliers final: 15 residues processed: 161 average time/residue: 1.4886 time to fit residues: 257.0659 Evaluate side-chains 160 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL 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 45 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL 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 189 SER 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 30 optimal weight: 5.9990 chunk 3 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 105 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.108514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.071748 restraints weight = 18491.793| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.54 r_work: 0.2935 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9271 Z= 0.242 Angle : 0.736 12.249 12580 Z= 0.367 Chirality : 0.042 0.196 1412 Planarity : 0.005 0.063 1609 Dihedral : 5.439 58.193 1302 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.40 % Favored : 95.26 % Rotamer: Outliers : 2.05 % Allowed : 29.53 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.25), residues: 1160 helix: 1.14 (0.26), residues: 464 sheet: -0.11 (0.34), residues: 215 loop : -1.18 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP R 115 HIS 0.006 0.001 HIS R 45 PHE 0.014 0.001 PHE R 402 TYR 0.025 0.001 TYR R 65 ARG 0.014 0.001 ARG N 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7957.61 seconds wall clock time: 141 minutes 16.02 seconds (8476.02 seconds total)