Starting phenix.real_space_refine on Thu Mar 13 12:52:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yw5_39623/03_2025/8yw5_39623.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yw5_39623/03_2025/8yw5_39623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yw5_39623/03_2025/8yw5_39623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yw5_39623/03_2025/8yw5_39623.map" model { file = "/net/cci-nas-00/data/ceres_data/8yw5_39623/03_2025/8yw5_39623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yw5_39623/03_2025/8yw5_39623.cif" } resolution = 2.84 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= 0.078 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 54 5.16 5 C 5691 2.51 5 N 1553 2.21 5 O 1639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8937 Number of models: 1 Model: "" Number of chains: 6 Chain: "P" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 237 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'2ML:plan-1': 1, 'AIB:plan-1': 2} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 2954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2954 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 11, 'TRANS': 367} Chain breaks: 2 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 122 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 106 Chain: "A" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1817 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 3 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 2552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2552 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "G" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 417 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 960 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 5.68, per 1000 atoms: 0.64 Number of scatterers: 8937 At special positions: 0 Unit cell: (77.112, 99.603, 168.147, 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 54 16.00 O 1639 8.00 N 1553 7.00 C 5691 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 67 " distance=2.03 Simple disulfide: pdb=" SG CYS R 58 " - pdb=" SG CYS R 100 " distance=2.03 Simple disulfide: pdb=" SG CYS R 224 " - pdb=" SG CYS R 294 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.1 seconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 41.4% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'P' and resid 1 through 28 removed outlier: 3.548A pdb=" N PHE P 6 " --> pdb=" O AIB P 2 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 47 Processing helix chain 'R' and resid 124 through 164 Processing helix chain 'R' and resid 171 through 203 Processing helix chain 'R' and resid 208 through 217 removed outlier: 3.926A pdb=" N VAL R 212 " --> pdb=" O ASP R 208 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER R 213 " --> pdb=" O ASP R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 253 Processing helix chain 'R' and resid 265 through 273 Processing helix chain 'R' and resid 275 through 290 Proline residue: R 281 - end of helix Processing helix chain 'R' and resid 300 through 305 Processing helix chain 'R' and resid 308 through 334 removed outlier: 3.544A pdb=" N PHE R 320 " --> pdb=" O LEU R 316 " (cutoff:3.500A) Processing helix chain 'R' and resid 343 through 351 Processing helix chain 'R' and resid 353 through 359 removed outlier: 4.090A pdb=" N LEU R 357 " --> pdb=" O THR R 353 " (cutoff:3.500A) Processing helix chain 'R' and resid 361 through 366 removed outlier: 3.983A pdb=" N PHE R 365 " --> pdb=" O HIS R 361 " (cutoff:3.500A) Processing helix chain 'R' and resid 380 through 402 removed outlier: 4.600A pdb=" N GLY R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LEU R 394 " --> pdb=" O SER R 390 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 419 Processing helix chain 'A' and resid 10 through 39 removed outlier: 3.543A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.522A pdb=" N ILE A 56 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.552A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.588A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 314 through 318 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.678A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.709A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.831A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.667A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.667A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.804A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 61 through 62 removed outlier: 3.953A pdb=" N THR R 61 " --> pdb=" O TRP R 68 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TRP R 68 " --> pdb=" O THR R 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'R' and resid 79 through 80 removed outlier: 3.911A pdb=" N ILE R 79 " --> pdb=" O VAL R 96 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 214 removed outlier: 6.640A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.220A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.573A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.144A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.943A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.705A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.514A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.651A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.645A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.826A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1314 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: 2.71 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2922 1.34 - 1.46: 2232 1.46 - 1.58: 3906 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 9133 Sorted by residual: bond pdb=" CA 2ML P 13 " pdb=" C 2ML P 13 " ideal model delta sigma weight residual 1.525 1.576 -0.051 2.10e-02 2.27e+03 5.89e+00 bond pdb=" N AIB P 2 " pdb=" CA AIB P 2 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.90e-02 2.77e+03 4.55e+00 bond pdb=" N AIB P 20 " pdb=" CA AIB P 20 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.90e-02 2.77e+03 4.45e+00 bond pdb=" C GLN R 113 " pdb=" N PRO R 114 " ideal model delta sigma weight residual 1.326 1.346 -0.020 1.44e-02 4.82e+03 1.86e+00 bond pdb=" C 2ML P 13 " pdb=" O 2ML P 13 " ideal model delta sigma weight residual 1.231 1.258 -0.027 2.00e-02 2.50e+03 1.80e+00 ... (remaining 9128 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 12069 1.22 - 2.45: 257 2.45 - 3.67: 54 3.67 - 4.90: 18 4.90 - 6.12: 5 Bond angle restraints: 12403 Sorted by residual: angle pdb=" N SER R 265 " pdb=" CA SER R 265 " pdb=" C SER R 265 " ideal model delta sigma weight residual 114.62 108.50 6.12 1.14e+00 7.69e-01 2.89e+01 angle pdb=" C GLN R 105 " pdb=" CA GLN R 105 " pdb=" CB GLN R 105 " ideal model delta sigma weight residual 116.54 110.68 5.86 1.15e+00 7.56e-01 2.60e+01 angle pdb=" C GLN R 293 " pdb=" CA GLN R 293 " pdb=" CB GLN R 293 " ideal model delta sigma weight residual 115.79 110.67 5.12 1.19e+00 7.06e-01 1.85e+01 angle pdb=" N VAL N 110 " pdb=" CA VAL N 110 " pdb=" C VAL N 110 " ideal model delta sigma weight residual 112.83 109.77 3.06 9.90e-01 1.02e+00 9.57e+00 angle pdb=" CA SER R 265 " pdb=" C SER R 265 " pdb=" N LEU R 266 " ideal model delta sigma weight residual 119.71 116.12 3.59 1.17e+00 7.31e-01 9.41e+00 ... (remaining 12398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 4929 16.00 - 31.99: 326 31.99 - 47.99: 76 47.99 - 63.99: 21 63.99 - 79.98: 4 Dihedral angle restraints: 5356 sinusoidal: 2015 harmonic: 3341 Sorted by residual: dihedral pdb=" CA LEU R 352 " pdb=" C LEU R 352 " pdb=" N THR R 353 " pdb=" CA THR R 353 " ideal model delta harmonic sigma weight residual 180.00 157.57 22.43 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 163.40 16.60 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" N LEU R 163 " pdb=" CA LEU R 163 " pdb=" CB LEU R 163 " pdb=" CG LEU R 163 " ideal model delta sinusoidal sigma weight residual -60.00 -119.97 59.97 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1078 0.044 - 0.088: 241 0.088 - 0.132: 68 0.132 - 0.175: 1 0.175 - 0.219: 1 Chirality restraints: 1389 Sorted by residual: chirality pdb=" CA 2ML P 13 " pdb=" C 2ML P 13 " pdb=" CB1 2ML P 13 " pdb=" CB2 2ML P 13 " both_signs ideal model delta sigma weight residual False -2.84 -3.06 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA PRO B 236 " pdb=" N PRO B 236 " pdb=" C PRO B 236 " pdb=" CB PRO B 236 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA VAL N 93 " pdb=" N VAL N 93 " pdb=" C VAL N 93 " pdb=" CB VAL N 93 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 1386 not shown) Planarity restraints: 1583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.028 5.00e-02 4.00e+02 4.16e-02 2.76e+00 pdb=" N PRO B 236 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 258 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO R 259 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 259 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 259 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 145 " 0.011 2.00e-02 2.50e+03 8.77e-03 1.54e+00 pdb=" CG TYR R 145 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR R 145 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR R 145 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR R 145 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR R 145 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR R 145 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR R 145 " 0.001 2.00e-02 2.50e+03 ... (remaining 1580 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 91 2.63 - 3.20: 7766 3.20 - 3.77: 13458 3.77 - 4.33: 19825 4.33 - 4.90: 32999 Nonbonded interactions: 74139 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.064 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.227 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.235 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.256 3.040 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.263 3.120 ... (remaining 74134 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.070 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:14.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 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 : 0.003 0.051 9133 Z= 0.218 Angle : 0.495 6.124 12403 Z= 0.269 Chirality : 0.040 0.219 1389 Planarity : 0.003 0.042 1583 Dihedral : 11.963 79.981 3185 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.79 % Allowed : 6.39 % Favored : 89.82 % 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: -0.41 (0.25), residues: 1127 helix: 0.11 (0.24), residues: 431 sheet: 0.05 (0.32), residues: 236 loop : -0.66 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.004 0.001 HIS R 170 PHE 0.018 0.001 PHE N 108 TYR 0.021 0.001 TYR R 145 ARG 0.003 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 1.013 Fit side-chains REVERT: R 37 LYS cc_start: 0.6467 (mmtt) cc_final: 0.6226 (mmtt) REVERT: R 144 MET cc_start: 0.8492 (tmm) cc_final: 0.8177 (tmm) REVERT: R 231 MET cc_start: 0.8440 (ttp) cc_final: 0.8123 (ttt) REVERT: R 263 PHE cc_start: 0.7483 (OUTLIER) cc_final: 0.7242 (m-10) REVERT: R 345 PHE cc_start: 0.6206 (OUTLIER) cc_final: 0.5820 (m-80) REVERT: R 415 TRP cc_start: 0.6145 (t-100) cc_final: 0.5505 (t-100) REVERT: A 370 GLU cc_start: 0.7920 (pp20) cc_final: 0.7661 (tm-30) REVERT: A 390 GLN cc_start: 0.8817 (mt0) cc_final: 0.8317 (mt0) REVERT: B 101 MET cc_start: 0.9006 (mtp) cc_final: 0.8737 (mtp) REVERT: B 234 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.7783 (m-80) outliers start: 35 outliers final: 19 residues processed: 145 average time/residue: 1.2504 time to fit residues: 193.6949 Evaluate side-chains 120 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 168 LYS Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 263 PHE Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 395 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.0770 chunk 84 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 0.0570 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 65 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 131 GLN R 293 GLN A 31 GLN A 357 HIS B 155 ASN B 259 GLN N 31 ASN N 120 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.192229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.143567 restraints weight = 8985.041| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.08 r_work: 0.3326 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9133 Z= 0.169 Angle : 0.536 9.450 12403 Z= 0.286 Chirality : 0.041 0.160 1389 Planarity : 0.004 0.041 1583 Dihedral : 7.321 59.296 1289 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.79 % Allowed : 10.94 % Favored : 85.27 % 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: 0.92 (0.26), residues: 1127 helix: 2.03 (0.24), residues: 427 sheet: 0.33 (0.34), residues: 235 loop : -0.55 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.002 0.001 HIS A 220 PHE 0.018 0.001 PHE A 212 TYR 0.020 0.001 TYR R 145 ARG 0.006 0.000 ARG R 334 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 1.029 Fit side-chains REVERT: R 37 LYS cc_start: 0.7529 (mmtt) cc_final: 0.7291 (mmtt) REVERT: R 277 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7999 (tt) REVERT: R 338 MET cc_start: 0.4208 (pmm) cc_final: 0.3583 (pmt) REVERT: R 345 PHE cc_start: 0.6545 (OUTLIER) cc_final: 0.6251 (m-80) REVERT: R 415 TRP cc_start: 0.6260 (t-100) cc_final: 0.5687 (t-100) REVERT: A 370 GLU cc_start: 0.7857 (pp20) cc_final: 0.7379 (pp20) REVERT: B 59 TYR cc_start: 0.8919 (OUTLIER) cc_final: 0.8663 (t80) REVERT: B 101 MET cc_start: 0.8955 (mtp) cc_final: 0.8685 (mtp) REVERT: B 197 ARG cc_start: 0.8066 (mtp180) cc_final: 0.7793 (mtt-85) REVERT: B 234 PHE cc_start: 0.9323 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: B 258 ASP cc_start: 0.7557 (t0) cc_final: 0.7341 (t0) REVERT: B 325 MET cc_start: 0.8982 (tpp) cc_final: 0.8721 (tpp) REVERT: N 120 GLN cc_start: 0.8117 (tp-100) cc_final: 0.7815 (tp40) outliers start: 35 outliers final: 18 residues processed: 123 average time/residue: 1.1117 time to fit residues: 147.1588 Evaluate side-chains 107 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 168 LYS Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 420 LEU Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 32 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 131 GLN R 293 GLN A 31 GLN A 357 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.191259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.142767 restraints weight = 9069.929| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.16 r_work: 0.3298 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9133 Z= 0.210 Angle : 0.532 9.866 12403 Z= 0.281 Chirality : 0.041 0.175 1389 Planarity : 0.004 0.041 1583 Dihedral : 6.917 59.116 1282 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.88 % Allowed : 11.92 % Favored : 83.21 % 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: 1.18 (0.26), residues: 1127 helix: 2.44 (0.24), residues: 427 sheet: 0.34 (0.34), residues: 236 loop : -0.55 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 170 PHE 0.018 0.002 PHE N 108 TYR 0.025 0.001 TYR R 145 ARG 0.007 0.000 ARG R 334 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 87 time to evaluate : 0.922 Fit side-chains REVERT: R 29 MET cc_start: 0.6880 (OUTLIER) cc_final: 0.3741 (tpt) REVERT: R 277 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8035 (tt) REVERT: R 345 PHE cc_start: 0.6525 (OUTLIER) cc_final: 0.6223 (m-80) REVERT: R 415 TRP cc_start: 0.6251 (t-100) cc_final: 0.5670 (t-100) REVERT: A 370 GLU cc_start: 0.7878 (pp20) cc_final: 0.7393 (pp20) REVERT: B 101 MET cc_start: 0.8916 (mtp) cc_final: 0.8581 (mtp) REVERT: B 137 ARG cc_start: 0.8168 (tpp-160) cc_final: 0.7574 (tpt170) REVERT: B 197 ARG cc_start: 0.8105 (mtp180) cc_final: 0.7869 (mtt-85) REVERT: B 234 PHE cc_start: 0.9332 (OUTLIER) cc_final: 0.7897 (m-80) REVERT: B 258 ASP cc_start: 0.7538 (t0) cc_final: 0.7301 (t0) REVERT: B 325 MET cc_start: 0.9056 (tpp) cc_final: 0.8812 (tpp) REVERT: N 80 TYR cc_start: 0.8037 (m-80) cc_final: 0.7582 (m-80) REVERT: N 120 GLN cc_start: 0.8142 (tp-100) cc_final: 0.7853 (tp40) outliers start: 45 outliers final: 21 residues processed: 124 average time/residue: 0.9719 time to fit residues: 130.9072 Evaluate side-chains 111 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 MET Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 168 LYS Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 420 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 131 GLN A 31 GLN A 357 HIS N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.191468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.143030 restraints weight = 8987.783| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.18 r_work: 0.3310 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9133 Z= 0.199 Angle : 0.521 10.940 12403 Z= 0.273 Chirality : 0.041 0.164 1389 Planarity : 0.003 0.040 1583 Dihedral : 6.670 59.872 1279 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.98 % Allowed : 12.89 % Favored : 82.12 % 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: 1.30 (0.26), residues: 1127 helix: 2.67 (0.24), residues: 427 sheet: 0.26 (0.34), residues: 239 loop : -0.55 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 170 PHE 0.016 0.001 PHE N 108 TYR 0.023 0.001 TYR R 145 ARG 0.009 0.000 ARG R 334 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 92 time to evaluate : 1.184 Fit side-chains REVERT: R 29 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.3778 (tpt) REVERT: R 145 TYR cc_start: 0.8347 (p90) cc_final: 0.7117 (p90) REVERT: R 231 MET cc_start: 0.8913 (ttt) cc_final: 0.8514 (ttt) REVERT: R 277 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8130 (tt) REVERT: R 338 MET cc_start: 0.3662 (pmm) cc_final: 0.1290 (mmm) REVERT: R 345 PHE cc_start: 0.6500 (OUTLIER) cc_final: 0.6192 (m-80) REVERT: R 415 TRP cc_start: 0.6072 (t-100) cc_final: 0.5489 (t-100) REVERT: A 370 GLU cc_start: 0.7891 (pp20) cc_final: 0.7371 (pp20) REVERT: B 49 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7981 (mtp85) REVERT: B 101 MET cc_start: 0.8897 (mtp) cc_final: 0.8667 (mtp) REVERT: B 137 ARG cc_start: 0.8159 (tpp-160) cc_final: 0.7554 (tpt170) REVERT: B 197 ARG cc_start: 0.8072 (mtp180) cc_final: 0.7848 (mtt-85) REVERT: B 234 PHE cc_start: 0.9336 (OUTLIER) cc_final: 0.8037 (m-80) REVERT: B 258 ASP cc_start: 0.7517 (t0) cc_final: 0.7302 (t0) REVERT: B 325 MET cc_start: 0.9062 (tpp) cc_final: 0.8847 (tpp) REVERT: N 80 TYR cc_start: 0.8002 (m-80) cc_final: 0.7585 (m-80) REVERT: N 120 GLN cc_start: 0.8141 (tp-100) cc_final: 0.7822 (tp40) outliers start: 46 outliers final: 21 residues processed: 130 average time/residue: 1.3524 time to fit residues: 190.3578 Evaluate side-chains 114 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 MET Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 168 LYS Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 420 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 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 131 GLN A 31 GLN A 357 HIS N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.190657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.132662 restraints weight = 8981.071| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.08 r_work: 0.3311 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9133 Z= 0.235 Angle : 0.535 10.168 12403 Z= 0.280 Chirality : 0.041 0.155 1389 Planarity : 0.004 0.042 1583 Dihedral : 6.725 59.811 1279 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.33 % Allowed : 14.73 % Favored : 80.93 % 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: 1.29 (0.26), residues: 1127 helix: 2.62 (0.24), residues: 433 sheet: 0.26 (0.33), residues: 239 loop : -0.55 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS R 170 PHE 0.019 0.002 PHE N 108 TYR 0.024 0.001 TYR R 145 ARG 0.010 0.000 ARG R 334 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 89 time to evaluate : 1.014 Fit side-chains REVERT: R 29 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.3722 (tpt) REVERT: R 145 TYR cc_start: 0.8275 (p90) cc_final: 0.6987 (p90) REVERT: R 231 MET cc_start: 0.8844 (ttt) cc_final: 0.8499 (ttt) REVERT: R 277 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8044 (tt) REVERT: R 345 PHE cc_start: 0.6347 (OUTLIER) cc_final: 0.6013 (m-80) REVERT: R 415 TRP cc_start: 0.6066 (t-100) cc_final: 0.5486 (t-100) REVERT: A 370 GLU cc_start: 0.7826 (pp20) cc_final: 0.7255 (pp20) REVERT: B 49 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7923 (mtp85) REVERT: B 137 ARG cc_start: 0.8081 (tpp-160) cc_final: 0.7444 (tpt170) REVERT: B 153 ASP cc_start: 0.8656 (m-30) cc_final: 0.8437 (m-30) REVERT: B 234 PHE cc_start: 0.9302 (OUTLIER) cc_final: 0.7973 (m-80) REVERT: B 258 ASP cc_start: 0.7451 (t0) cc_final: 0.7244 (t0) REVERT: B 325 MET cc_start: 0.9071 (tpp) cc_final: 0.8834 (tpp) REVERT: N 80 TYR cc_start: 0.7896 (m-80) cc_final: 0.7213 (m-80) REVERT: N 120 GLN cc_start: 0.8151 (tp-100) cc_final: 0.7855 (tp40) outliers start: 40 outliers final: 23 residues processed: 123 average time/residue: 1.1994 time to fit residues: 159.5040 Evaluate side-chains 114 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 MET Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 168 LYS Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 420 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 20 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 0.0980 chunk 81 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 357 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.190058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.132088 restraints weight = 8954.781| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.07 r_work: 0.3297 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9133 Z= 0.271 Angle : 0.560 12.077 12403 Z= 0.291 Chirality : 0.042 0.156 1389 Planarity : 0.004 0.042 1583 Dihedral : 6.836 59.852 1279 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.77 % Allowed : 14.73 % Favored : 80.50 % 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: 1.20 (0.26), residues: 1127 helix: 2.48 (0.24), residues: 439 sheet: 0.26 (0.33), residues: 237 loop : -0.59 (0.32), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS R 170 PHE 0.020 0.002 PHE N 108 TYR 0.026 0.002 TYR R 145 ARG 0.011 0.000 ARG R 334 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 86 time to evaluate : 1.020 Fit side-chains REVERT: R 29 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.3698 (tpt) REVERT: R 145 TYR cc_start: 0.8297 (p90) cc_final: 0.7122 (p90) REVERT: R 231 MET cc_start: 0.8856 (ttt) cc_final: 0.8525 (ttt) REVERT: R 277 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7971 (tt) REVERT: R 338 MET cc_start: 0.3950 (pmm) cc_final: 0.1557 (mmm) REVERT: R 345 PHE cc_start: 0.6334 (OUTLIER) cc_final: 0.5997 (m-80) REVERT: R 415 TRP cc_start: 0.6041 (t-100) cc_final: 0.5452 (t-100) REVERT: A 370 GLU cc_start: 0.7876 (pp20) cc_final: 0.7195 (pp20) REVERT: B 49 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7883 (mtp85) REVERT: B 123 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8689 (mt) REVERT: B 137 ARG cc_start: 0.8079 (tpp-160) cc_final: 0.7464 (tpt170) REVERT: B 153 ASP cc_start: 0.8599 (m-30) cc_final: 0.8388 (m-30) REVERT: B 234 PHE cc_start: 0.9301 (OUTLIER) cc_final: 0.7978 (m-80) REVERT: B 258 ASP cc_start: 0.7466 (t0) cc_final: 0.7254 (t0) REVERT: B 325 MET cc_start: 0.9088 (tpp) cc_final: 0.8847 (tpp) outliers start: 44 outliers final: 24 residues processed: 124 average time/residue: 1.2291 time to fit residues: 165.2485 Evaluate side-chains 115 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 MET Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 168 LYS Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 420 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 75 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 131 GLN R 293 GLN A 31 GLN A 357 HIS ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.190300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.141981 restraints weight = 9052.712| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.18 r_work: 0.3278 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9133 Z= 0.249 Angle : 0.549 11.018 12403 Z= 0.287 Chirality : 0.042 0.154 1389 Planarity : 0.004 0.046 1583 Dihedral : 6.816 59.881 1279 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.23 % Allowed : 15.38 % Favored : 80.39 % 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: 1.18 (0.26), residues: 1127 helix: 2.48 (0.24), residues: 439 sheet: 0.20 (0.33), residues: 239 loop : -0.60 (0.32), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS R 170 PHE 0.020 0.002 PHE N 108 TYR 0.024 0.001 TYR R 145 ARG 0.013 0.000 ARG R 334 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 87 time to evaluate : 0.919 Fit side-chains REVERT: R 29 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.3913 (tpt) REVERT: R 145 TYR cc_start: 0.8420 (p90) cc_final: 0.7247 (p90) REVERT: R 231 MET cc_start: 0.8914 (ttt) cc_final: 0.8567 (ttt) REVERT: R 277 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8103 (tt) REVERT: R 345 PHE cc_start: 0.6569 (OUTLIER) cc_final: 0.6230 (m-80) REVERT: R 415 TRP cc_start: 0.6135 (t-100) cc_final: 0.5563 (t-100) REVERT: A 370 GLU cc_start: 0.7947 (pp20) cc_final: 0.7287 (pp20) REVERT: B 49 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7955 (mtp85) REVERT: B 137 ARG cc_start: 0.8166 (tpp-160) cc_final: 0.7582 (tpt170) REVERT: B 153 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8463 (m-30) REVERT: B 234 PHE cc_start: 0.9347 (OUTLIER) cc_final: 0.8060 (m-80) REVERT: B 258 ASP cc_start: 0.7550 (t0) cc_final: 0.7339 (t0) REVERT: B 325 MET cc_start: 0.9112 (tpp) cc_final: 0.8898 (tpp) REVERT: N 120 GLN cc_start: 0.8165 (tp-100) cc_final: 0.7939 (tp40) outliers start: 39 outliers final: 24 residues processed: 119 average time/residue: 1.0673 time to fit residues: 137.0689 Evaluate side-chains 114 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 MET Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 168 LYS Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 420 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 47 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 11 optimal weight: 0.0970 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 131 GLN A 31 GLN A 357 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.191704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.143139 restraints weight = 9126.604| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.22 r_work: 0.3279 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9133 Z= 0.191 Angle : 0.525 12.113 12403 Z= 0.274 Chirality : 0.040 0.148 1389 Planarity : 0.003 0.055 1583 Dihedral : 6.672 59.579 1279 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.12 % Allowed : 15.82 % Favored : 80.07 % 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: 1.32 (0.26), residues: 1127 helix: 2.69 (0.24), residues: 433 sheet: 0.25 (0.34), residues: 237 loop : -0.57 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS R 170 PHE 0.015 0.001 PHE N 108 TYR 0.018 0.001 TYR R 145 ARG 0.013 0.000 ARG R 334 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 89 time to evaluate : 0.972 Fit side-chains REVERT: R 29 MET cc_start: 0.7077 (OUTLIER) cc_final: 0.4048 (tpt) REVERT: R 231 MET cc_start: 0.8883 (ttt) cc_final: 0.8463 (ttt) REVERT: R 277 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8197 (tt) REVERT: R 338 MET cc_start: 0.3877 (pmm) cc_final: 0.1773 (mmt) REVERT: R 345 PHE cc_start: 0.6491 (OUTLIER) cc_final: 0.6129 (m-80) REVERT: R 415 TRP cc_start: 0.6114 (t-100) cc_final: 0.5562 (t-100) REVERT: A 370 GLU cc_start: 0.7863 (pp20) cc_final: 0.7258 (pp20) REVERT: B 49 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7933 (mtp85) REVERT: B 137 ARG cc_start: 0.8086 (tpp-160) cc_final: 0.7513 (tpt170) REVERT: B 234 PHE cc_start: 0.9328 (OUTLIER) cc_final: 0.8105 (m-80) REVERT: N 120 GLN cc_start: 0.8143 (tp-100) cc_final: 0.7908 (tp40) outliers start: 38 outliers final: 21 residues processed: 122 average time/residue: 1.0626 time to fit residues: 140.6054 Evaluate side-chains 110 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 MET Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 168 LYS Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 420 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 5 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 131 GLN R 204 GLN R 293 GLN A 31 GLN A 357 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.191492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.133515 restraints weight = 9075.161| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.10 r_work: 0.3326 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9133 Z= 0.203 Angle : 0.532 13.253 12403 Z= 0.277 Chirality : 0.041 0.148 1389 Planarity : 0.004 0.054 1583 Dihedral : 6.466 59.829 1277 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.68 % Allowed : 16.03 % Favored : 80.28 % 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: 1.29 (0.26), residues: 1127 helix: 2.69 (0.24), residues: 433 sheet: 0.16 (0.34), residues: 238 loop : -0.57 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 170 PHE 0.016 0.001 PHE N 108 TYR 0.021 0.001 TYR R 145 ARG 0.015 0.000 ARG R 334 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 87 time to evaluate : 1.627 Fit side-chains REVERT: R 29 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.3930 (tpt) REVERT: R 231 MET cc_start: 0.8834 (ttt) cc_final: 0.8460 (ttt) REVERT: R 277 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8054 (tt) REVERT: R 338 MET cc_start: 0.4003 (pmm) cc_final: 0.1604 (mmm) REVERT: R 345 PHE cc_start: 0.6304 (OUTLIER) cc_final: 0.5968 (m-80) REVERT: R 415 TRP cc_start: 0.6018 (t-100) cc_final: 0.5425 (t-100) REVERT: A 370 GLU cc_start: 0.7818 (pp20) cc_final: 0.7137 (pp20) REVERT: B 49 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7891 (mtp85) REVERT: B 137 ARG cc_start: 0.8067 (tpp-160) cc_final: 0.7443 (tpt170) REVERT: B 234 PHE cc_start: 0.9294 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: B 325 MET cc_start: 0.9016 (tpp) cc_final: 0.8736 (mpp) outliers start: 34 outliers final: 21 residues processed: 116 average time/residue: 1.2688 time to fit residues: 157.8494 Evaluate side-chains 109 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 MET Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 168 LYS Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 420 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 0.0770 chunk 23 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 110 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 131 GLN R 204 GLN A 31 GLN A 357 HIS N 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.192724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.134910 restraints weight = 9079.770| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.10 r_work: 0.3346 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9133 Z= 0.173 Angle : 0.515 13.266 12403 Z= 0.268 Chirality : 0.040 0.146 1389 Planarity : 0.003 0.060 1583 Dihedral : 6.333 59.914 1277 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.14 % Allowed : 16.79 % Favored : 80.07 % 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: 1.36 (0.26), residues: 1127 helix: 2.75 (0.24), residues: 433 sheet: 0.19 (0.34), residues: 238 loop : -0.53 (0.32), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS R 170 PHE 0.014 0.001 PHE A 212 TYR 0.024 0.001 TYR N 60 ARG 0.015 0.000 ARG R 334 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 0.995 Fit side-chains REVERT: R 29 MET cc_start: 0.6919 (OUTLIER) cc_final: 0.4058 (tpt) REVERT: R 231 MET cc_start: 0.8834 (ttt) cc_final: 0.8434 (ttt) REVERT: R 277 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8037 (tt) REVERT: R 338 MET cc_start: 0.4003 (pmm) cc_final: 0.1477 (mmm) REVERT: R 345 PHE cc_start: 0.6296 (OUTLIER) cc_final: 0.5969 (m-80) REVERT: R 415 TRP cc_start: 0.6042 (t-100) cc_final: 0.5434 (t-100) REVERT: A 370 GLU cc_start: 0.7802 (pp20) cc_final: 0.7105 (pp20) REVERT: B 49 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7896 (mtp85) REVERT: B 137 ARG cc_start: 0.8054 (tpp-160) cc_final: 0.7427 (tpt170) REVERT: B 234 PHE cc_start: 0.9279 (OUTLIER) cc_final: 0.8048 (m-80) REVERT: B 325 MET cc_start: 0.9003 (tpp) cc_final: 0.8718 (mpp) outliers start: 29 outliers final: 19 residues processed: 114 average time/residue: 1.2301 time to fit residues: 150.8385 Evaluate side-chains 106 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 MET Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 168 LYS Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 420 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 71 optimal weight: 0.0370 chunk 92 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 131 GLN R 204 GLN R 293 GLN R 404 ASN A 31 GLN A 357 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.190936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.132679 restraints weight = 9073.273| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.10 r_work: 0.3312 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9133 Z= 0.254 Angle : 0.565 14.276 12403 Z= 0.291 Chirality : 0.042 0.152 1389 Planarity : 0.004 0.055 1583 Dihedral : 6.270 59.872 1273 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.93 % Allowed : 17.33 % Favored : 79.74 % 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: 1.26 (0.26), residues: 1127 helix: 2.64 (0.24), residues: 433 sheet: 0.15 (0.34), residues: 238 loop : -0.56 (0.32), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS R 250 PHE 0.019 0.002 PHE N 108 TYR 0.024 0.002 TYR R 145 ARG 0.015 0.000 ARG R 334 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7446.66 seconds wall clock time: 129 minutes 38.85 seconds (7778.85 seconds total)