Starting phenix.real_space_refine on Wed Sep 17 13:36:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yw5_39623/09_2025/8yw5_39623.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yw5_39623/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yw5_39623/09_2025/8yw5_39623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yw5_39623/09_2025/8yw5_39623.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yw5_39623/09_2025/8yw5_39623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yw5_39623/09_2025/8yw5_39623.map" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.078 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'AIB:plan-1': 2, '2ML:plan-1': 1} 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: {'HIS:plan': 2, 'ARG:plan': 8, 'TRP:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 1, 'GLU:plan': 4, 'PHE:plan': 2} 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, 'ASP:plan': 1, 'ARG:plan': 4} 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: 1.99, per 1000 atoms: 0.22 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: 0.61 Conformation dependent library (CDL) restraints added in 260.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.30 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: 1.42 Time building geometry restraints manager: 0.78 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.580 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.020 ------------------------------------------------------------------------------- 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 9138 Z= 0.144 Angle : 0.496 6.124 12413 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (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 ARG 0.003 0.000 ARG N 72 TYR 0.021 0.001 TYR R 145 PHE 0.018 0.001 PHE N 108 TRP 0.013 0.001 TRP B 99 HIS 0.004 0.001 HIS R 170 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9133) covalent geometry : angle 0.49531 (12403) SS BOND : bond 0.00193 ( 5) SS BOND : angle 0.83653 ( 10) hydrogen bonds : bond 0.23998 ( 458) hydrogen bonds : angle 8.32088 ( 1314) *********************** 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 : 0.305 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: 0.7241 (m-10) REVERT: R 345 PHE cc_start: 0.6206 (OUTLIER) cc_final: 0.5822 (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: 0.5371 time to fit residues: 82.9465 Evaluate side-chains 122 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 108 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.188794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.140038 restraints weight = 9037.575| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.23 r_work: 0.3246 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9138 Z= 0.209 Angle : 0.619 10.360 12413 Z= 0.326 Chirality : 0.044 0.175 1389 Planarity : 0.005 0.044 1583 Dihedral : 7.606 58.910 1289 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.98 % Allowed : 10.73 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.26), residues: 1127 helix: 1.72 (0.24), residues: 432 sheet: 0.30 (0.34), residues: 232 loop : -0.65 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 334 TYR 0.028 0.002 TYR R 145 PHE 0.024 0.002 PHE N 108 TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS R 170 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 9133) covalent geometry : angle 0.61823 (12403) SS BOND : bond 0.00170 ( 5) SS BOND : angle 0.97796 ( 10) hydrogen bonds : bond 0.05896 ( 458) hydrogen bonds : angle 5.15334 ( 1314) *********************** 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 138 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 92 time to evaluate : 0.326 Fit side-chains REVERT: R 37 LYS cc_start: 0.7517 (mmtt) cc_final: 0.7250 (mmtt) REVERT: R 277 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8107 (tt) REVERT: R 338 MET cc_start: 0.4048 (pmm) cc_final: 0.3417 (pmt) REVERT: R 345 PHE cc_start: 0.6590 (OUTLIER) cc_final: 0.6296 (m-80) REVERT: R 415 TRP cc_start: 0.6265 (t-100) cc_final: 0.5736 (t-100) REVERT: A 370 GLU cc_start: 0.7957 (pp20) cc_final: 0.7475 (pp20) REVERT: B 59 TYR cc_start: 0.8988 (OUTLIER) cc_final: 0.8642 (t80) REVERT: B 153 ASP cc_start: 0.8854 (m-30) cc_final: 0.8554 (m-30) REVERT: B 197 ARG cc_start: 0.8104 (mtp180) cc_final: 0.7770 (mtt-85) REVERT: B 234 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.7894 (m-80) REVERT: B 258 ASP cc_start: 0.7638 (t0) cc_final: 0.7400 (t0) REVERT: B 325 MET cc_start: 0.9067 (tpp) cc_final: 0.8803 (tpp) REVERT: N 120 GLN cc_start: 0.8154 (tp-100) cc_final: 0.7854 (tp40) outliers start: 46 outliers final: 20 residues processed: 131 average time/residue: 0.4950 time to fit residues: 69.5130 Evaluate side-chains 110 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 306 ILE Chi-restraints excluded: chain R residue 345 PHE 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 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 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 125 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 10 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 66 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 53 optimal weight: 0.0170 overall best weight: 0.5220 ------------------------------------------------------------------------------- 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 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.191851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.134223 restraints weight = 9021.447| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.12 r_work: 0.3337 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9138 Z= 0.116 Angle : 0.511 10.160 12413 Z= 0.271 Chirality : 0.041 0.184 1389 Planarity : 0.003 0.041 1583 Dihedral : 7.017 59.828 1283 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.77 % Allowed : 12.24 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.26), residues: 1127 helix: 2.45 (0.24), residues: 427 sheet: 0.34 (0.34), residues: 234 loop : -0.60 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 334 TYR 0.018 0.001 TYR R 145 PHE 0.015 0.001 PHE A 212 TRP 0.019 0.001 TRP B 82 HIS 0.002 0.001 HIS R 340 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 9133) covalent geometry : angle 0.51086 (12403) SS BOND : bond 0.00116 ( 5) SS BOND : angle 0.80694 ( 10) hydrogen bonds : bond 0.04384 ( 458) hydrogen bonds : angle 4.60688 ( 1314) *********************** 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 138 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 94 time to evaluate : 0.315 Fit side-chains REVERT: R 29 MET cc_start: 0.6573 (OUTLIER) cc_final: 0.3494 (tpt) REVERT: R 37 LYS cc_start: 0.7507 (mmtt) cc_final: 0.7286 (mmtt) REVERT: R 145 TYR cc_start: 0.8179 (p90) cc_final: 0.6801 (p90) REVERT: R 277 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7920 (tt) REVERT: R 345 PHE cc_start: 0.6338 (OUTLIER) cc_final: 0.6004 (m-80) REVERT: R 415 TRP cc_start: 0.6171 (t-100) cc_final: 0.5580 (t-100) REVERT: A 370 GLU cc_start: 0.7777 (pp20) cc_final: 0.7273 (pp20) REVERT: B 49 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7900 (mtp85) REVERT: B 59 TYR cc_start: 0.8906 (OUTLIER) cc_final: 0.8699 (t80) REVERT: B 176 GLN cc_start: 0.9235 (tt0) cc_final: 0.9012 (tt0) REVERT: B 197 ARG cc_start: 0.7942 (mtp180) cc_final: 0.7689 (mtt-85) REVERT: B 234 PHE cc_start: 0.9260 (OUTLIER) cc_final: 0.7901 (m-80) REVERT: B 258 ASP cc_start: 0.7454 (t0) cc_final: 0.7203 (t0) REVERT: B 325 MET cc_start: 0.8977 (tpp) cc_final: 0.8642 (mpp) REVERT: N 80 TYR cc_start: 0.7926 (m-80) cc_final: 0.7493 (m-80) outliers start: 44 outliers final: 17 residues processed: 130 average time/residue: 0.4258 time to fit residues: 59.7868 Evaluate side-chains 113 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 104 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 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 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 = 0.190325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.141920 restraints weight = 9123.055| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.23 r_work: 0.3262 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9138 Z= 0.150 Angle : 0.545 12.156 12413 Z= 0.285 Chirality : 0.041 0.154 1389 Planarity : 0.004 0.041 1583 Dihedral : 6.985 59.716 1281 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.55 % Allowed : 14.08 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.26), residues: 1127 helix: 2.55 (0.24), residues: 427 sheet: 0.29 (0.34), residues: 236 loop : -0.58 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 334 TYR 0.025 0.001 TYR R 145 PHE 0.020 0.002 PHE N 108 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS R 170 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9133) covalent geometry : angle 0.54455 (12403) SS BOND : bond 0.00144 ( 5) SS BOND : angle 0.81985 ( 10) hydrogen bonds : bond 0.04495 ( 458) hydrogen bonds : angle 4.57198 ( 1314) *********************** 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 134 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 92 time to evaluate : 0.251 Fit side-chains REVERT: R 29 MET cc_start: 0.6764 (OUTLIER) cc_final: 0.3674 (tpt) REVERT: R 37 LYS cc_start: 0.7609 (mmtt) cc_final: 0.7314 (mmtt) REVERT: R 145 TYR cc_start: 0.8275 (p90) cc_final: 0.7021 (p90) REVERT: R 277 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8084 (tt) REVERT: R 338 MET cc_start: 0.3621 (pmm) cc_final: 0.2926 (pmt) REVERT: R 345 PHE cc_start: 0.6460 (OUTLIER) cc_final: 0.6105 (m-80) REVERT: R 415 TRP cc_start: 0.6255 (t-100) cc_final: 0.5669 (t-100) REVERT: A 370 GLU cc_start: 0.7866 (pp20) cc_final: 0.7330 (pp20) REVERT: B 49 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7864 (mtp85) REVERT: B 137 ARG cc_start: 0.8034 (tpp-160) cc_final: 0.7445 (tpt170) REVERT: B 197 ARG cc_start: 0.8013 (mtp180) cc_final: 0.7772 (mtt-85) REVERT: B 234 PHE cc_start: 0.9312 (OUTLIER) cc_final: 0.8058 (m-80) REVERT: B 258 ASP cc_start: 0.7471 (t0) cc_final: 0.7265 (t0) REVERT: B 325 MET cc_start: 0.9017 (tpp) cc_final: 0.8814 (tpp) REVERT: N 80 TYR cc_start: 0.8009 (m-80) cc_final: 0.7650 (m-80) REVERT: N 120 GLN cc_start: 0.8067 (tp-100) cc_final: 0.7840 (tp40) outliers start: 42 outliers final: 19 residues processed: 129 average time/residue: 0.4450 time to fit residues: 62.0220 Evaluate side-chains 115 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 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 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 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 24 optimal weight: 0.0470 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 0.4980 chunk 64 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 55 optimal weight: 0.0970 chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- 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 B 176 GLN N 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.192995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.135511 restraints weight = 8995.159| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.09 r_work: 0.3356 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9138 Z= 0.105 Angle : 0.492 11.266 12413 Z= 0.259 Chirality : 0.040 0.148 1389 Planarity : 0.003 0.045 1583 Dihedral : 6.565 59.766 1279 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.26), residues: 1127 helix: 2.83 (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 ARG 0.012 0.000 ARG R 334 TYR 0.019 0.001 TYR R 145 PHE 0.014 0.001 PHE A 212 TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS R 170 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 9133) covalent geometry : angle 0.49152 (12403) SS BOND : bond 0.00101 ( 5) SS BOND : angle 0.68522 ( 10) hydrogen bonds : bond 0.03833 ( 458) hydrogen bonds : angle 4.32347 ( 1314) *********************** 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 133 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 93 time to evaluate : 0.332 Fit side-chains REVERT: R 29 MET cc_start: 0.6634 (OUTLIER) cc_final: 0.3616 (tpt) REVERT: R 37 LYS cc_start: 0.7569 (mmtt) cc_final: 0.7329 (mmtt) REVERT: R 145 TYR cc_start: 0.8176 (p90) cc_final: 0.6862 (p90) REVERT: R 277 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8054 (tt) REVERT: R 345 PHE cc_start: 0.6288 (OUTLIER) cc_final: 0.5950 (m-80) REVERT: R 415 TRP cc_start: 0.5998 (t-100) cc_final: 0.5414 (t-100) REVERT: A 370 GLU cc_start: 0.7787 (pp20) cc_final: 0.7176 (pp20) REVERT: B 49 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7888 (mtp85) REVERT: B 137 ARG cc_start: 0.8000 (tpp-160) cc_final: 0.7329 (tpt170) REVERT: B 197 ARG cc_start: 0.7931 (mtp180) cc_final: 0.7690 (mtt-85) REVERT: B 234 PHE cc_start: 0.9263 (OUTLIER) cc_final: 0.7911 (m-80) REVERT: B 258 ASP cc_start: 0.7447 (t0) cc_final: 0.7219 (t0) REVERT: B 325 MET cc_start: 0.8990 (tpp) cc_final: 0.8658 (mpp) REVERT: N 80 TYR cc_start: 0.7848 (m-80) cc_final: 0.7523 (m-80) REVERT: N 120 GLN cc_start: 0.8081 (tp-100) cc_final: 0.7876 (tp40) outliers start: 40 outliers final: 18 residues processed: 126 average time/residue: 0.4890 time to fit residues: 66.3403 Evaluate side-chains 105 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 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 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 44 optimal weight: 0.0170 chunk 109 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.2024 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.190279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.141869 restraints weight = 9063.683| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.23 r_work: 0.3245 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9138 Z= 0.165 Angle : 0.556 11.823 12413 Z= 0.289 Chirality : 0.042 0.156 1389 Planarity : 0.004 0.039 1583 Dihedral : 6.519 59.764 1276 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.23 % Allowed : 15.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.26), residues: 1127 helix: 2.61 (0.24), residues: 433 sheet: 0.26 (0.34), residues: 239 loop : -0.58 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 334 TYR 0.027 0.002 TYR R 145 PHE 0.022 0.002 PHE N 108 TRP 0.013 0.002 TRP B 82 HIS 0.004 0.001 HIS R 170 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 9133) covalent geometry : angle 0.55588 (12403) SS BOND : bond 0.00159 ( 5) SS BOND : angle 0.79565 ( 10) hydrogen bonds : bond 0.04408 ( 458) hydrogen bonds : angle 4.45604 ( 1314) *********************** 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: 39 poor density : 91 time to evaluate : 0.202 Fit side-chains REVERT: R 29 MET cc_start: 0.6988 (OUTLIER) cc_final: 0.3873 (tpt) REVERT: R 37 LYS cc_start: 0.7779 (mmtt) cc_final: 0.7488 (mmtt) REVERT: R 145 TYR cc_start: 0.8352 (p90) cc_final: 0.7239 (p90) REVERT: R 277 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8241 (tt) REVERT: R 338 MET cc_start: 0.3683 (pmm) cc_final: 0.1205 (mmm) REVERT: R 345 PHE cc_start: 0.6521 (OUTLIER) cc_final: 0.6164 (m-80) REVERT: R 415 TRP cc_start: 0.6136 (t-100) cc_final: 0.5573 (t-100) REVERT: A 370 GLU cc_start: 0.7916 (pp20) cc_final: 0.7312 (pp20) REVERT: B 49 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7914 (mtp85) REVERT: B 137 ARG cc_start: 0.8064 (tpp-160) cc_final: 0.7587 (tpt170) REVERT: B 153 ASP cc_start: 0.8690 (m-30) cc_final: 0.8401 (m-30) REVERT: B 234 PHE cc_start: 0.9339 (OUTLIER) cc_final: 0.8088 (m-80) REVERT: B 325 MET cc_start: 0.9070 (tpp) cc_final: 0.8842 (tpp) REVERT: N 120 GLN cc_start: 0.8136 (tp-100) cc_final: 0.7926 (tp40) outliers start: 39 outliers final: 20 residues processed: 127 average time/residue: 0.4696 time to fit residues: 64.0780 Evaluate side-chains 113 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 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 B residue 49 ARG 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 165 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 51 optimal weight: 0.0370 chunk 23 optimal weight: 0.5980 chunk 95 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 ** B 237 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 = 0.4143 r_free = 0.4143 target = 0.191828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.143164 restraints weight = 9056.466| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.21 r_work: 0.3302 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9138 Z= 0.118 Angle : 0.519 11.956 12413 Z= 0.272 Chirality : 0.040 0.149 1389 Planarity : 0.003 0.050 1583 Dihedral : 6.412 59.512 1276 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.01 % Allowed : 15.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.26), residues: 1127 helix: 2.72 (0.24), residues: 433 sheet: 0.30 (0.34), residues: 237 loop : -0.56 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG R 334 TYR 0.020 0.001 TYR R 145 PHE 0.015 0.001 PHE A 212 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 170 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9133) covalent geometry : angle 0.51915 (12403) SS BOND : bond 0.00103 ( 5) SS BOND : angle 0.65757 ( 10) hydrogen bonds : bond 0.03964 ( 458) hydrogen bonds : angle 4.33376 ( 1314) *********************** 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: 37 poor density : 89 time to evaluate : 0.337 Fit side-chains REVERT: R 29 MET cc_start: 0.6849 (OUTLIER) cc_final: 0.3783 (tpt) REVERT: R 37 LYS cc_start: 0.7606 (mmtt) cc_final: 0.7334 (mmtt) REVERT: R 145 TYR cc_start: 0.8225 (p90) cc_final: 0.7033 (p90) REVERT: R 277 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8177 (tt) REVERT: R 345 PHE cc_start: 0.6405 (OUTLIER) cc_final: 0.6041 (m-80) REVERT: R 415 TRP cc_start: 0.6123 (t-100) cc_final: 0.5556 (t-100) REVERT: A 370 GLU cc_start: 0.7819 (pp20) cc_final: 0.7230 (pp20) REVERT: B 49 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7874 (mtp85) REVERT: B 137 ARG cc_start: 0.7973 (tpp-160) cc_final: 0.7355 (tpt170) REVERT: B 234 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.8065 (m-80) REVERT: N 80 TYR cc_start: 0.7841 (m-80) cc_final: 0.7374 (m-80) REVERT: N 120 GLN cc_start: 0.8110 (tp-100) cc_final: 0.7889 (tp40) outliers start: 37 outliers final: 20 residues processed: 122 average time/residue: 0.4486 time to fit residues: 59.0785 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 : 0.338 ------------------------------------------------------------------------------- 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 165 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE 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 75 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 71 optimal weight: 0.0670 chunk 76 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.4148 r_free = 0.4148 target = 0.192411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.144121 restraints weight = 9044.733| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.22 r_work: 0.3306 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9138 Z= 0.115 Angle : 0.518 12.788 12413 Z= 0.269 Chirality : 0.040 0.148 1389 Planarity : 0.003 0.055 1583 Dihedral : 6.342 59.821 1276 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.58 % Allowed : 16.90 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.26), residues: 1127 helix: 2.76 (0.24), residues: 433 sheet: 0.25 (0.34), residues: 239 loop : -0.54 (0.32), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG R 334 TYR 0.021 0.001 TYR N 60 PHE 0.015 0.001 PHE A 212 TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS R 170 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9133) covalent geometry : angle 0.51815 (12403) SS BOND : bond 0.00123 ( 5) SS BOND : angle 0.64074 ( 10) hydrogen bonds : bond 0.03829 ( 458) hydrogen bonds : angle 4.25915 ( 1314) *********************** 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 125 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 0.340 Fit side-chains REVERT: R 29 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.3973 (tpt) REVERT: R 37 LYS cc_start: 0.7496 (mmtt) cc_final: 0.7254 (mmtt) REVERT: R 277 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8179 (tt) REVERT: R 338 MET cc_start: 0.3843 (pmm) cc_final: 0.1699 (mmt) REVERT: R 345 PHE cc_start: 0.6389 (OUTLIER) cc_final: 0.6020 (m-80) REVERT: R 415 TRP cc_start: 0.6146 (t-100) cc_final: 0.5576 (t-100) REVERT: A 370 GLU cc_start: 0.7821 (pp20) cc_final: 0.7210 (pp20) REVERT: B 49 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7887 (mtp85) REVERT: B 137 ARG cc_start: 0.7992 (tpp-160) cc_final: 0.7386 (tpt170) REVERT: B 234 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.8062 (m-80) REVERT: B 325 MET cc_start: 0.8916 (tpp) cc_final: 0.8642 (mpp) REVERT: N 80 TYR cc_start: 0.7734 (m-80) cc_final: 0.7153 (m-80) outliers start: 33 outliers final: 20 residues processed: 121 average time/residue: 0.5393 time to fit residues: 69.6880 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 : 0.249 ------------------------------------------------------------------------------- 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 165 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE 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 59 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 N 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.191663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.143350 restraints weight = 9001.156| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.21 r_work: 0.3273 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9138 Z= 0.129 Angle : 0.534 13.743 12413 Z= 0.276 Chirality : 0.041 0.151 1389 Planarity : 0.003 0.054 1583 Dihedral : 6.387 59.873 1276 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.90 % Allowed : 16.79 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.26), residues: 1127 helix: 2.74 (0.24), residues: 433 sheet: 0.27 (0.34), residues: 238 loop : -0.54 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG R 334 TYR 0.022 0.001 TYR R 145 PHE 0.015 0.001 PHE N 108 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 170 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9133) covalent geometry : angle 0.53385 (12403) SS BOND : bond 0.00127 ( 5) SS BOND : angle 0.66496 ( 10) hydrogen bonds : bond 0.03962 ( 458) hydrogen bonds : angle 4.28904 ( 1314) *********************** 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: 36 poor density : 85 time to evaluate : 0.332 Fit side-chains REVERT: R 29 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.4026 (tpt) REVERT: R 37 LYS cc_start: 0.7498 (mmtt) cc_final: 0.7240 (mmtt) REVERT: R 145 TYR cc_start: 0.8244 (p90) cc_final: 0.7072 (p90) REVERT: R 277 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8183 (tt) REVERT: R 338 MET cc_start: 0.3822 (pmm) cc_final: 0.1279 (mmt) REVERT: R 345 PHE cc_start: 0.6379 (OUTLIER) cc_final: 0.6025 (m-80) REVERT: R 415 TRP cc_start: 0.6121 (t-100) cc_final: 0.5541 (t-100) REVERT: A 370 GLU cc_start: 0.7830 (pp20) cc_final: 0.7226 (pp20) REVERT: B 49 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7893 (mtp85) REVERT: B 137 ARG cc_start: 0.7991 (tpp-160) cc_final: 0.7527 (tpt170) REVERT: B 234 PHE cc_start: 0.9318 (OUTLIER) cc_final: 0.8070 (m-80) REVERT: B 325 MET cc_start: 0.9018 (tpp) cc_final: 0.8698 (mpp) REVERT: N 80 TYR cc_start: 0.7769 (m-80) cc_final: 0.7386 (m-80) outliers start: 36 outliers final: 19 residues processed: 116 average time/residue: 0.4977 time to fit residues: 62.1847 Evaluate side-chains 108 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 B residue 49 ARG 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 165 THR 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 92 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.188414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.129935 restraints weight = 9085.776| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.11 r_work: 0.3271 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 9138 Z= 0.240 Angle : 0.641 15.181 12413 Z= 0.329 Chirality : 0.045 0.162 1389 Planarity : 0.004 0.049 1583 Dihedral : 6.611 59.512 1274 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.47 % Allowed : 17.23 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.26), residues: 1127 helix: 2.30 (0.24), residues: 440 sheet: 0.14 (0.34), residues: 240 loop : -0.64 (0.32), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 334 TYR 0.030 0.002 TYR R 145 PHE 0.025 0.002 PHE N 108 TRP 0.014 0.002 TRP A 281 HIS 0.005 0.001 HIS R 170 Details of bonding type rmsd covalent geometry : bond 0.00591 ( 9133) covalent geometry : angle 0.64100 (12403) SS BOND : bond 0.00217 ( 5) SS BOND : angle 0.95791 ( 10) hydrogen bonds : bond 0.04950 ( 458) hydrogen bonds : angle 4.66019 ( 1314) ********************** 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: 32 poor density : 87 time to evaluate : 0.338 Fit side-chains REVERT: R 29 MET cc_start: 0.6778 (OUTLIER) cc_final: 0.3714 (tpt) REVERT: R 37 LYS cc_start: 0.7406 (mmtt) cc_final: 0.7109 (mmtt) REVERT: R 277 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8037 (tt) REVERT: R 338 MET cc_start: 0.4043 (pmm) cc_final: 0.1447 (mmt) REVERT: R 345 PHE cc_start: 0.6312 (OUTLIER) cc_final: 0.5945 (m-80) REVERT: R 415 TRP cc_start: 0.6132 (t-100) cc_final: 0.5521 (t-100) REVERT: A 370 GLU cc_start: 0.7928 (pp20) cc_final: 0.7221 (pp20) REVERT: B 49 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7879 (mtp85) REVERT: B 137 ARG cc_start: 0.8058 (tpp-160) cc_final: 0.7478 (tpt170) REVERT: B 234 PHE cc_start: 0.9326 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: B 258 ASP cc_start: 0.7584 (t0) cc_final: 0.7324 (t0) outliers start: 32 outliers final: 19 residues processed: 115 average time/residue: 0.5667 time to fit residues: 69.5232 Evaluate side-chains 109 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 B residue 49 ARG Chi-restraints excluded: chain B residue 70 LEU 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 165 THR 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 19 optimal weight: 0.0870 chunk 52 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.191748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.133829 restraints weight = 8952.211| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.08 r_work: 0.3333 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9138 Z= 0.114 Angle : 0.528 13.621 12413 Z= 0.275 Chirality : 0.040 0.152 1389 Planarity : 0.004 0.062 1583 Dihedral : 6.326 59.512 1274 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.93 % Allowed : 17.77 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.26), residues: 1127 helix: 2.63 (0.24), residues: 433 sheet: 0.12 (0.34), residues: 240 loop : -0.57 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG R 334 TYR 0.023 0.001 TYR N 60 PHE 0.015 0.001 PHE N 108 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS R 170 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9133) covalent geometry : angle 0.52800 (12403) SS BOND : bond 0.00103 ( 5) SS BOND : angle 0.67059 ( 10) hydrogen bonds : bond 0.03900 ( 458) hydrogen bonds : angle 4.33924 ( 1314) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3064.69 seconds wall clock time: 52 minutes 55.51 seconds (3175.51 seconds total)