Starting phenix.real_space_refine on Sun Jul 27 09:45:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vbi_31880/07_2025/7vbi_31880.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vbi_31880/07_2025/7vbi_31880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vbi_31880/07_2025/7vbi_31880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vbi_31880/07_2025/7vbi_31880.map" model { file = "/net/cci-nas-00/data/ceres_data/7vbi_31880/07_2025/7vbi_31880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vbi_31880/07_2025/7vbi_31880.cif" } resolution = 3.0 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= -0.001 sd= 0.108 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 5882 2.51 5 N 1596 2.21 5 O 1691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9223 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1891 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 2 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'AIB:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "R" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3115 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 13, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2591 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Time building chain proxies: 5.70, per 1000 atoms: 0.62 Number of scatterers: 9223 At special positions: 0 Unit cell: (76.041, 100.674, 173.502, 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 1691 8.00 N 1596 7.00 C 5882 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.04 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.02 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: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 40.8% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.547A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.758A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS A 58 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.565A pdb=" N ASN A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.646A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.416A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.833A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.912A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 Processing helix chain 'P' and resid 2 through 29 removed outlier: 3.669A pdb=" N VAL P 23 " --> pdb=" O GLN P 19 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA P 28 " --> pdb=" O GLN P 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 51 removed outlier: 3.577A pdb=" N TYR R 42 " --> pdb=" O LYS R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 169 removed outlier: 3.583A pdb=" N PHE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 205 removed outlier: 3.725A pdb=" N PHE R 195 " --> pdb=" O ALA R 191 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE R 196 " --> pdb=" O LEU R 192 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 214 Processing helix chain 'R' and resid 219 through 222 Processing helix chain 'R' and resid 223 through 256 removed outlier: 4.037A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL R 237 " --> pdb=" O MET R 233 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA R 238 " --> pdb=" O GLN R 234 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN R 240 " --> pdb=" O CYS R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 275 removed outlier: 3.761A pdb=" N SER R 271 " --> pdb=" O ARG R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 280 removed outlier: 3.786A pdb=" N PHE R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 291 Processing helix chain 'R' and resid 293 through 298 removed outlier: 4.496A pdb=" N CYS R 296 " --> pdb=" O ASP R 293 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP R 297 " --> pdb=" O GLU R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 336 Proline residue: R 312 - end of helix removed outlier: 3.663A pdb=" N ALA R 316 " --> pdb=" O PRO R 312 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N CYS R 329 " --> pdb=" O VAL R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 346 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 377 through 389 Processing helix chain 'R' and resid 390 through 403 removed outlier: 3.635A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 422 removed outlier: 3.962A pdb=" N GLU R 412 " --> pdb=" O GLU R 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.877A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 4.006A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 22 removed outlier: 3.794A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.521A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.185A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.626A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.454A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 82 through 83 Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.573A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.670A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.928A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.698A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.996A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.351A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 275 through 278 removed outlier: 4.063A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1221 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: 2.53 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2583 1.33 - 1.46: 2487 1.46 - 1.58: 4288 1.58 - 1.71: 0 1.71 - 1.84: 73 Bond restraints: 9431 Sorted by residual: bond pdb=" C PHE B 234 " pdb=" N PHE B 235 " ideal model delta sigma weight residual 1.328 1.274 0.054 1.44e-02 4.82e+03 1.41e+01 bond pdb=" CA PHE A 238 " pdb=" CB PHE A 238 " ideal model delta sigma weight residual 1.526 1.471 0.055 1.51e-02 4.39e+03 1.33e+01 bond pdb=" CG1 ILE B 81 " pdb=" CD1 ILE B 81 " ideal model delta sigma weight residual 1.513 1.398 0.115 3.90e-02 6.57e+02 8.62e+00 bond pdb=" C PHE B 235 " pdb=" N PRO B 236 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.19e-02 7.06e+03 7.67e+00 bond pdb=" CG1 ILE B 58 " pdb=" CD1 ILE B 58 " ideal model delta sigma weight residual 1.513 1.410 0.103 3.90e-02 6.57e+02 6.91e+00 ... (remaining 9426 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 12321 2.56 - 5.12: 400 5.12 - 7.69: 48 7.69 - 10.25: 12 10.25 - 12.81: 6 Bond angle restraints: 12787 Sorted by residual: angle pdb=" C THR A 319 " pdb=" N THR A 320 " pdb=" CA THR A 320 " ideal model delta sigma weight residual 120.51 130.15 -9.64 1.45e+00 4.76e-01 4.42e+01 angle pdb=" O ASP B 291 " pdb=" C ASP B 291 " pdb=" N PHE B 292 " ideal model delta sigma weight residual 122.39 129.37 -6.98 1.29e+00 6.01e-01 2.93e+01 angle pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta sigma weight residual 120.39 127.58 -7.19 1.39e+00 5.18e-01 2.67e+01 angle pdb=" C ARG N 98 " pdb=" N CYS N 99 " pdb=" CA CYS N 99 " ideal model delta sigma weight residual 122.74 110.14 12.60 2.44e+00 1.68e-01 2.67e+01 angle pdb=" N VAL R 405 " pdb=" CA VAL R 405 " pdb=" C VAL R 405 " ideal model delta sigma weight residual 113.10 108.34 4.76 9.70e-01 1.06e+00 2.41e+01 ... (remaining 12782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.13: 4972 18.13 - 36.25: 488 36.25 - 54.38: 83 54.38 - 72.50: 21 72.50 - 90.63: 9 Dihedral angle restraints: 5573 sinusoidal: 2202 harmonic: 3371 Sorted by residual: dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 126 " pdb=" CB CYS R 126 " ideal model delta sinusoidal sigma weight residual 93.00 162.50 -69.50 1 1.00e+01 1.00e-02 6.24e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -144.63 -35.37 0 5.00e+00 4.00e-02 5.00e+01 dihedral pdb=" CA LEU R 217 " pdb=" C LEU R 217 " pdb=" N LEU R 218 " pdb=" CA LEU R 218 " ideal model delta harmonic sigma weight residual 180.00 146.84 33.16 0 5.00e+00 4.00e-02 4.40e+01 ... (remaining 5570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 873 0.050 - 0.101: 396 0.101 - 0.151: 110 0.151 - 0.201: 23 0.201 - 0.251: 10 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CB ILE N 51 " pdb=" CA ILE N 51 " pdb=" CG1 ILE N 51 " pdb=" CG2 ILE N 51 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB ILE A 308 " pdb=" CA ILE A 308 " pdb=" CG1 ILE A 308 " pdb=" CG2 ILE A 308 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA VAL R 282 " pdb=" N VAL R 282 " pdb=" C VAL R 282 " pdb=" CB VAL R 282 " both_signs ideal model delta sigma weight residual False 2.44 2.21 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1409 not shown) Planarity restraints: 1623 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 384 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C LEU R 384 " -0.058 2.00e-02 2.50e+03 pdb=" O LEU R 384 " 0.022 2.00e-02 2.50e+03 pdb=" N PHE R 385 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO R 55 " -0.051 5.00e-02 4.00e+02 7.55e-02 9.12e+00 pdb=" N PRO R 56 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO R 56 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO R 56 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 395 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.71e+00 pdb=" C GLY R 395 " 0.051 2.00e-02 2.50e+03 pdb=" O GLY R 395 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU R 396 " -0.017 2.00e-02 2.50e+03 ... (remaining 1620 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 745 2.73 - 3.27: 8443 3.27 - 3.81: 14905 3.81 - 4.36: 18454 4.36 - 4.90: 32142 Nonbonded interactions: 74689 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.181 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.265 3.040 nonbonded pdb=" O TYR R 69 " pdb=" OH TYR R 88 " model vdw 2.267 3.040 nonbonded pdb=" NE2 HIS A 362 " pdb=" OD2 ASP A 378 " model vdw 2.290 3.120 nonbonded pdb=" OE2 GLU P 3 " pdb=" OH TYR R 152 " model vdw 2.315 3.040 ... (remaining 74684 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.820 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 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 : 0.011 0.115 9437 Z= 0.482 Angle : 1.128 12.808 12799 Z= 0.634 Chirality : 0.063 0.251 1412 Planarity : 0.008 0.076 1623 Dihedral : 14.914 90.630 3377 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.81 % Allowed : 7.42 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.18 % 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: -3.46 (0.20), residues: 1133 helix: -2.64 (0.18), residues: 429 sheet: -1.08 (0.32), residues: 229 loop : -2.44 (0.23), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP R 72 HIS 0.020 0.003 HIS A 357 PHE 0.044 0.004 PHE N 108 TYR 0.027 0.003 TYR R 148 ARG 0.014 0.001 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.19655 ( 424) hydrogen bonds : angle 7.43376 ( 1221) SS BOND : bond 0.00604 ( 6) SS BOND : angle 2.74903 ( 12) covalent geometry : bond 0.01118 ( 9431) covalent geometry : angle 1.12522 (12787) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 1.004 Fit side-chains REVERT: A 272 LEU cc_start: 0.8286 (mt) cc_final: 0.8052 (mm) REVERT: A 339 TYR cc_start: 0.8678 (m-80) cc_final: 0.8439 (m-80) REVERT: N 34 MET cc_start: 0.8108 (mmm) cc_final: 0.7733 (mmm) REVERT: N 46 GLU cc_start: 0.7187 (mp0) cc_final: 0.6890 (mp0) REVERT: N 94 TYR cc_start: 0.8429 (m-80) cc_final: 0.8141 (m-80) REVERT: N 95 TYR cc_start: 0.8513 (m-80) cc_final: 0.8165 (m-80) REVERT: P 9 ASP cc_start: 0.8069 (m-30) cc_final: 0.7473 (m-30) REVERT: R 146 ILE cc_start: 0.8759 (mt) cc_final: 0.8484 (mp) REVERT: R 267 ARG cc_start: 0.7041 (tpt170) cc_final: 0.6324 (mpp80) REVERT: R 336 LYS cc_start: 0.8081 (mttp) cc_final: 0.7778 (mmtm) REVERT: R 348 ARG cc_start: 0.7395 (tpm170) cc_final: 0.6602 (mtp180) REVERT: R 376 ARG cc_start: 0.7880 (ptp-170) cc_final: 0.7274 (mtt90) REVERT: R 415 LYS cc_start: 0.7048 (mtmt) cc_final: 0.6697 (mttt) REVERT: B 42 ARG cc_start: 0.7356 (ttp-110) cc_final: 0.7059 (ttm-80) outliers start: 8 outliers final: 4 residues processed: 177 average time/residue: 1.3415 time to fit residues: 252.5992 Evaluate side-chains 135 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.6980 chunk 84 optimal weight: 0.0570 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 35 GLN A 227 GLN A 279 ASN A 371 ASN N 1 GLN N 31 ASN N 77 ASN R 37 GLN R 45 GLN R 140 GLN R 211 GLN R 221 GLN B 119 ASN B 132 ASN B 230 ASN B 239 ASN G 24 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.193054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.149243 restraints weight = 10073.276| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.74 r_work: 0.3323 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9437 Z= 0.140 Angle : 0.613 8.982 12799 Z= 0.329 Chirality : 0.041 0.150 1412 Planarity : 0.005 0.062 1623 Dihedral : 5.867 50.026 1273 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.76 % Allowed : 13.72 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.71 (0.23), residues: 1133 helix: -0.50 (0.24), residues: 433 sheet: -0.52 (0.32), residues: 242 loop : -2.04 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 214 HIS 0.006 0.001 HIS A 357 PHE 0.017 0.001 PHE N 108 TYR 0.022 0.001 TYR R 148 ARG 0.007 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.04831 ( 424) hydrogen bonds : angle 4.92256 ( 1221) SS BOND : bond 0.00325 ( 6) SS BOND : angle 2.68450 ( 12) covalent geometry : bond 0.00311 ( 9431) covalent geometry : angle 0.60802 (12787) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 0.991 Fit side-chains REVERT: A 272 LEU cc_start: 0.8367 (mt) cc_final: 0.8114 (mm) REVERT: A 283 ARG cc_start: 0.7820 (ptp-110) cc_final: 0.7533 (mtm110) REVERT: A 347 ARG cc_start: 0.7808 (ttp-170) cc_final: 0.7580 (ttp80) REVERT: N 34 MET cc_start: 0.8467 (mmm) cc_final: 0.8076 (mmm) REVERT: N 39 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.8008 (tt0) REVERT: N 46 GLU cc_start: 0.8191 (mp0) cc_final: 0.7951 (mp0) REVERT: P 3 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7108 (mm-30) REVERT: R 146 ILE cc_start: 0.8806 (mt) cc_final: 0.8582 (mp) REVERT: R 167 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7677 (pp) REVERT: R 202 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7463 (tttp) REVERT: R 267 ARG cc_start: 0.7288 (tpt170) cc_final: 0.6347 (mpp80) REVERT: R 336 LYS cc_start: 0.7862 (mttp) cc_final: 0.7594 (mmtm) REVERT: R 376 ARG cc_start: 0.7719 (ptp-170) cc_final: 0.6984 (mtt90) REVERT: R 387 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.5829 (mt-10) REVERT: B 42 ARG cc_start: 0.7289 (ttp-110) cc_final: 0.6769 (ttm-80) REVERT: B 217 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7835 (pmm) REVERT: G 21 MET cc_start: 0.5278 (OUTLIER) cc_final: 0.4984 (tmm) outliers start: 37 outliers final: 14 residues processed: 165 average time/residue: 1.4076 time to fit residues: 247.1561 Evaluate side-chains 157 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 63 optimal weight: 0.2980 chunk 91 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 279 ASN A 387 HIS N 31 ASN N 77 ASN R 37 GLN ** R 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 394 GLN B 230 ASN 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 = 0.187954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.135338 restraints weight = 10237.028| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.41 r_work: 0.3316 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9437 Z= 0.189 Angle : 0.640 10.345 12799 Z= 0.339 Chirality : 0.043 0.204 1412 Planarity : 0.005 0.061 1623 Dihedral : 5.633 40.048 1269 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.07 % Allowed : 15.35 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.21 (0.24), residues: 1133 helix: 0.27 (0.25), residues: 433 sheet: -0.48 (0.32), residues: 242 loop : -2.00 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 214 HIS 0.005 0.001 HIS B 142 PHE 0.017 0.002 PHE N 108 TYR 0.023 0.002 TYR R 148 ARG 0.008 0.000 ARG R 44 Details of bonding type rmsd hydrogen bonds : bond 0.04886 ( 424) hydrogen bonds : angle 4.71397 ( 1221) SS BOND : bond 0.00704 ( 6) SS BOND : angle 2.84206 ( 12) covalent geometry : bond 0.00443 ( 9431) covalent geometry : angle 0.63403 (12787) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 272 LEU cc_start: 0.8392 (mt) cc_final: 0.8163 (mp) REVERT: A 283 ARG cc_start: 0.7931 (ptp-110) cc_final: 0.7601 (mtm110) REVERT: A 308 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7775 (tp) REVERT: A 356 ARG cc_start: 0.7159 (mtm110) cc_final: 0.6928 (mtm110) REVERT: A 386 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8363 (ttm) REVERT: N 34 MET cc_start: 0.8616 (mmm) cc_final: 0.8224 (mmm) REVERT: N 39 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: N 46 GLU cc_start: 0.8573 (mp0) cc_final: 0.8270 (mp0) REVERT: N 95 TYR cc_start: 0.8648 (m-80) cc_final: 0.8430 (m-80) REVERT: P 3 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7108 (mm-30) REVERT: R 44 ARG cc_start: 0.8569 (ttp80) cc_final: 0.8174 (ttp80) REVERT: R 146 ILE cc_start: 0.8855 (mt) cc_final: 0.8612 (mp) REVERT: R 167 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7554 (pp) REVERT: R 202 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7431 (tttp) REVERT: R 267 ARG cc_start: 0.7326 (tpt170) cc_final: 0.6231 (mpp80) REVERT: R 336 LYS cc_start: 0.7797 (mttp) cc_final: 0.7414 (mmtm) REVERT: R 348 ARG cc_start: 0.7475 (tpm-80) cc_final: 0.6215 (mtp180) REVERT: R 376 ARG cc_start: 0.7796 (ptp-170) cc_final: 0.7103 (mtt90) REVERT: R 387 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6039 (mt-10) REVERT: B 42 ARG cc_start: 0.7671 (ttp-110) cc_final: 0.7003 (ttm-80) REVERT: B 70 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8790 (pt) REVERT: B 171 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8552 (mm) REVERT: B 217 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7710 (pmm) REVERT: G 21 MET cc_start: 0.5165 (tmt) cc_final: 0.4869 (tmm) outliers start: 40 outliers final: 17 residues processed: 163 average time/residue: 1.7841 time to fit residues: 309.3140 Evaluate side-chains 155 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 53 optimal weight: 0.7980 chunk 99 optimal weight: 0.0970 chunk 90 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 43 optimal weight: 30.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN R 37 GLN B 230 ASN B 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.189552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.135556 restraints weight = 10124.771| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.52 r_work: 0.3310 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9437 Z= 0.133 Angle : 0.563 6.757 12799 Z= 0.300 Chirality : 0.041 0.146 1412 Planarity : 0.004 0.062 1623 Dihedral : 5.213 37.253 1269 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.27 % Allowed : 17.07 % Favored : 78.66 % 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: -0.71 (0.24), residues: 1133 helix: 0.73 (0.25), residues: 436 sheet: -0.11 (0.33), residues: 234 loop : -1.86 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 214 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.018 0.001 TYR R 148 ARG 0.005 0.000 ARG R 44 Details of bonding type rmsd hydrogen bonds : bond 0.04277 ( 424) hydrogen bonds : angle 4.49772 ( 1221) SS BOND : bond 0.00246 ( 6) SS BOND : angle 1.45756 ( 12) covalent geometry : bond 0.00305 ( 9431) covalent geometry : angle 0.56171 (12787) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 LEU cc_start: 0.8201 (mt) cc_final: 0.7955 (mp) REVERT: A 283 ARG cc_start: 0.7664 (ptp-110) cc_final: 0.7353 (mtm110) REVERT: A 308 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7465 (mt) REVERT: A 356 ARG cc_start: 0.7134 (mtm110) cc_final: 0.6917 (mtm110) REVERT: A 386 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8167 (ttm) REVERT: N 34 MET cc_start: 0.8411 (mmm) cc_final: 0.8039 (mmm) REVERT: N 46 GLU cc_start: 0.8339 (mp0) cc_final: 0.7939 (mp0) REVERT: P 3 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6841 (mm-30) REVERT: R 146 ILE cc_start: 0.8760 (mt) cc_final: 0.8527 (mp) REVERT: R 202 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7313 (tptp) REVERT: R 267 ARG cc_start: 0.7187 (tpt170) cc_final: 0.6202 (mpp80) REVERT: R 336 LYS cc_start: 0.7673 (mttp) cc_final: 0.7291 (mmtm) REVERT: R 348 ARG cc_start: 0.7318 (tpm-80) cc_final: 0.6124 (mtp180) REVERT: R 364 GLU cc_start: 0.7805 (mp0) cc_final: 0.7388 (mp0) REVERT: R 376 ARG cc_start: 0.7542 (ptp-170) cc_final: 0.6872 (mmt90) REVERT: R 387 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.5849 (mt-10) REVERT: B 42 ARG cc_start: 0.7518 (ttp-110) cc_final: 0.7071 (ttm-80) REVERT: B 70 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8621 (pt) REVERT: B 100 VAL cc_start: 0.9082 (OUTLIER) cc_final: 0.8828 (p) REVERT: B 217 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7671 (pmm) REVERT: G 21 MET cc_start: 0.4978 (OUTLIER) cc_final: 0.4723 (tmm) outliers start: 42 outliers final: 18 residues processed: 169 average time/residue: 1.3181 time to fit residues: 238.2130 Evaluate side-chains 158 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 279 ASN N 77 ASN B 75 GLN B 230 ASN B 239 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.189761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.130387 restraints weight = 10219.856| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.29 r_work: 0.3263 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9437 Z= 0.190 Angle : 0.610 8.739 12799 Z= 0.322 Chirality : 0.043 0.157 1412 Planarity : 0.004 0.063 1623 Dihedral : 5.296 37.243 1269 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.57 % Allowed : 18.80 % Favored : 76.63 % 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: -0.56 (0.24), residues: 1133 helix: 0.87 (0.25), residues: 437 sheet: 0.01 (0.33), residues: 229 loop : -1.78 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.022 0.002 PHE N 108 TYR 0.022 0.002 TYR R 148 ARG 0.008 0.000 ARG R 44 Details of bonding type rmsd hydrogen bonds : bond 0.04688 ( 424) hydrogen bonds : angle 4.49788 ( 1221) SS BOND : bond 0.00140 ( 6) SS BOND : angle 1.20822 ( 12) covalent geometry : bond 0.00446 ( 9431) covalent geometry : angle 0.60921 (12787) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 134 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 272 LEU cc_start: 0.8352 (mt) cc_final: 0.8130 (mp) REVERT: A 283 ARG cc_start: 0.7777 (ptp-110) cc_final: 0.7372 (mtm110) REVERT: A 308 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7679 (tp) REVERT: A 356 ARG cc_start: 0.7096 (mtm110) cc_final: 0.6849 (mtm110) REVERT: A 386 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8171 (ttm) REVERT: N 34 MET cc_start: 0.8403 (mmm) cc_final: 0.8098 (mmm) REVERT: N 39 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.8019 (tt0) REVERT: N 79 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7097 (tp) REVERT: P 3 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6865 (mm-30) REVERT: R 44 ARG cc_start: 0.8269 (ttp80) cc_final: 0.7904 (ttp80) REVERT: R 146 ILE cc_start: 0.8824 (mt) cc_final: 0.8598 (mp) REVERT: R 202 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7460 (tttp) REVERT: R 267 ARG cc_start: 0.7273 (tpt170) cc_final: 0.6311 (mpp80) REVERT: R 303 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7896 (mtt) REVERT: R 336 LYS cc_start: 0.7773 (mttp) cc_final: 0.7387 (mmtm) REVERT: R 348 ARG cc_start: 0.7438 (tpm-80) cc_final: 0.6213 (mtp180) REVERT: R 376 ARG cc_start: 0.7708 (ptp-170) cc_final: 0.7088 (mtt90) REVERT: R 387 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6037 (mt-10) REVERT: R 418 GLU cc_start: 0.7064 (tp30) cc_final: 0.6763 (tm-30) REVERT: B 42 ARG cc_start: 0.7627 (ttp-110) cc_final: 0.7176 (ttm-80) REVERT: B 70 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8779 (pt) REVERT: B 100 VAL cc_start: 0.9143 (OUTLIER) cc_final: 0.8898 (p) REVERT: B 171 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8399 (mm) REVERT: B 217 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7760 (pmm) REVERT: G 21 MET cc_start: 0.5034 (OUTLIER) cc_final: 0.4830 (tmm) outliers start: 45 outliers final: 19 residues processed: 161 average time/residue: 1.2277 time to fit residues: 211.3065 Evaluate side-chains 154 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 303 MET Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 0.0270 chunk 62 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 279 ASN N 77 ASN R 112 GLN B 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.191849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.134715 restraints weight = 10058.269| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.69 r_work: 0.3279 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9437 Z= 0.123 Angle : 0.563 8.500 12799 Z= 0.299 Chirality : 0.041 0.151 1412 Planarity : 0.004 0.065 1623 Dihedral : 5.069 37.211 1269 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.37 % Allowed : 19.92 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.25), residues: 1133 helix: 1.09 (0.25), residues: 442 sheet: 0.21 (0.34), residues: 229 loop : -1.74 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE N 108 TYR 0.019 0.001 TYR N 95 ARG 0.004 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 424) hydrogen bonds : angle 4.37758 ( 1221) SS BOND : bond 0.00154 ( 6) SS BOND : angle 0.93086 ( 12) covalent geometry : bond 0.00274 ( 9431) covalent geometry : angle 0.56224 (12787) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 135 time to evaluate : 1.111 Fit side-chains REVERT: A 272 LEU cc_start: 0.8261 (mt) cc_final: 0.8007 (mp) REVERT: A 283 ARG cc_start: 0.7648 (ptp-110) cc_final: 0.7278 (mtm110) REVERT: A 308 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7474 (mt) REVERT: A 356 ARG cc_start: 0.7143 (mtm110) cc_final: 0.6855 (mtm110) REVERT: A 392 GLU cc_start: 0.7874 (mp0) cc_final: 0.7610 (mm-30) REVERT: N 34 MET cc_start: 0.8414 (mmm) cc_final: 0.8042 (mmm) REVERT: N 39 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7990 (tt0) REVERT: N 46 GLU cc_start: 0.8311 (mp0) cc_final: 0.8020 (mp0) REVERT: N 79 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6992 (tp) REVERT: P 3 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6824 (mm-30) REVERT: R 41 GLU cc_start: 0.8344 (pp20) cc_final: 0.7684 (pp20) REVERT: R 68 GLU cc_start: 0.5218 (tt0) cc_final: 0.4899 (tt0) REVERT: R 146 ILE cc_start: 0.8763 (mt) cc_final: 0.8506 (mp) REVERT: R 267 ARG cc_start: 0.7287 (tpt170) cc_final: 0.6272 (mpp80) REVERT: R 336 LYS cc_start: 0.7671 (mttp) cc_final: 0.7267 (mmtm) REVERT: R 348 ARG cc_start: 0.7336 (tpm-80) cc_final: 0.6090 (mtp180) REVERT: R 376 ARG cc_start: 0.7478 (ptp-170) cc_final: 0.6818 (mtt90) REVERT: R 387 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.5913 (mt-10) REVERT: R 418 GLU cc_start: 0.6969 (tp30) cc_final: 0.6671 (tm-30) REVERT: B 42 ARG cc_start: 0.7620 (ttp-110) cc_final: 0.7107 (ttm-80) REVERT: B 70 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8621 (pt) REVERT: B 100 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8857 (p) REVERT: B 171 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8340 (mm) REVERT: B 217 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7695 (pmm) outliers start: 43 outliers final: 15 residues processed: 161 average time/residue: 1.2755 time to fit residues: 219.6618 Evaluate side-chains 150 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN R 37 GLN R 45 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.190938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.133656 restraints weight = 10188.184| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.65 r_work: 0.3268 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9437 Z= 0.136 Angle : 0.564 7.967 12799 Z= 0.299 Chirality : 0.041 0.168 1412 Planarity : 0.004 0.065 1623 Dihedral : 4.988 40.838 1269 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.25 % Allowed : 21.44 % Favored : 75.30 % 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: -0.10 (0.25), residues: 1133 helix: 1.31 (0.26), residues: 438 sheet: 0.30 (0.34), residues: 234 loop : -1.66 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.019 0.001 PHE B 292 TYR 0.018 0.001 TYR N 95 ARG 0.004 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 424) hydrogen bonds : angle 4.33423 ( 1221) SS BOND : bond 0.00103 ( 6) SS BOND : angle 0.97485 ( 12) covalent geometry : bond 0.00310 ( 9431) covalent geometry : angle 0.56339 (12787) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 1.217 Fit side-chains REVERT: A 272 LEU cc_start: 0.8272 (mt) cc_final: 0.8040 (mp) REVERT: A 283 ARG cc_start: 0.7682 (ptp-110) cc_final: 0.7309 (mtm110) REVERT: A 308 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7525 (mt) REVERT: A 356 ARG cc_start: 0.7133 (mtm110) cc_final: 0.6865 (mtm110) REVERT: A 392 GLU cc_start: 0.7851 (mp0) cc_final: 0.7622 (mm-30) REVERT: N 34 MET cc_start: 0.8402 (mmm) cc_final: 0.8051 (mmm) REVERT: N 39 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.8013 (tt0) REVERT: N 46 GLU cc_start: 0.8340 (mp0) cc_final: 0.8049 (mp0) REVERT: N 79 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6947 (tp) REVERT: P 3 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6847 (mm-30) REVERT: R 41 GLU cc_start: 0.8420 (pp20) cc_final: 0.8027 (pp20) REVERT: R 146 ILE cc_start: 0.8768 (mt) cc_final: 0.8477 (mp) REVERT: R 267 ARG cc_start: 0.7287 (tpt170) cc_final: 0.6301 (mpp80) REVERT: R 336 LYS cc_start: 0.7661 (mttp) cc_final: 0.7349 (mmtm) REVERT: R 348 ARG cc_start: 0.7357 (tpm-80) cc_final: 0.6131 (mtp180) REVERT: R 376 ARG cc_start: 0.7420 (ptp-170) cc_final: 0.6797 (mtt90) REVERT: R 387 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.5915 (mt-10) REVERT: R 418 GLU cc_start: 0.6998 (tp30) cc_final: 0.6690 (tm-30) REVERT: B 42 ARG cc_start: 0.7611 (ttp-110) cc_final: 0.7143 (ttm-80) REVERT: B 70 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8650 (pt) REVERT: B 100 VAL cc_start: 0.9056 (OUTLIER) cc_final: 0.8832 (p) REVERT: B 134 ARG cc_start: 0.7358 (ptp-170) cc_final: 0.7144 (ptp-110) REVERT: B 171 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8377 (mm) REVERT: B 217 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7746 (pmm) REVERT: G 21 MET cc_start: 0.3769 (tmm) cc_final: 0.3473 (tpt) outliers start: 32 outliers final: 18 residues processed: 149 average time/residue: 1.5246 time to fit residues: 243.6244 Evaluate side-chains 158 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 382 ILE Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 29 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 42 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN R 263 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.192224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.134987 restraints weight = 10303.541| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.67 r_work: 0.3314 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9437 Z= 0.117 Angle : 0.546 7.716 12799 Z= 0.289 Chirality : 0.040 0.158 1412 Planarity : 0.004 0.065 1623 Dihedral : 4.869 42.887 1269 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.15 % Allowed : 22.05 % Favored : 74.80 % 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: 0.06 (0.25), residues: 1133 helix: 1.50 (0.26), residues: 438 sheet: 0.37 (0.33), residues: 234 loop : -1.62 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.017 0.001 TYR N 95 ARG 0.005 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 424) hydrogen bonds : angle 4.23063 ( 1221) SS BOND : bond 0.00100 ( 6) SS BOND : angle 0.88697 ( 12) covalent geometry : bond 0.00264 ( 9431) covalent geometry : angle 0.54607 (12787) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 1.060 Fit side-chains REVERT: A 272 LEU cc_start: 0.8270 (mt) cc_final: 0.8031 (mp) REVERT: A 308 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7489 (mt) REVERT: A 331 ASP cc_start: 0.8024 (t0) cc_final: 0.7636 (t0) REVERT: A 343 ASP cc_start: 0.7387 (m-30) cc_final: 0.7023 (m-30) REVERT: A 392 GLU cc_start: 0.7862 (mp0) cc_final: 0.7658 (mm-30) REVERT: N 34 MET cc_start: 0.8411 (mmm) cc_final: 0.8018 (mmm) REVERT: N 46 GLU cc_start: 0.8359 (mp0) cc_final: 0.8115 (mp0) REVERT: N 79 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6952 (tp) REVERT: P 3 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6792 (mm-30) REVERT: R 41 GLU cc_start: 0.8418 (pp20) cc_final: 0.7791 (pp20) REVERT: R 146 ILE cc_start: 0.8744 (mt) cc_final: 0.8466 (mp) REVERT: R 267 ARG cc_start: 0.7304 (tpt170) cc_final: 0.6274 (mpp80) REVERT: R 294 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6525 (pp20) REVERT: R 336 LYS cc_start: 0.7670 (mttp) cc_final: 0.7341 (mmtm) REVERT: R 348 ARG cc_start: 0.7327 (tpm-80) cc_final: 0.6095 (mtp180) REVERT: R 376 ARG cc_start: 0.7449 (ptp-170) cc_final: 0.6816 (mtt90) REVERT: R 387 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.5873 (mt-10) REVERT: R 418 GLU cc_start: 0.6960 (tp30) cc_final: 0.6653 (tm-30) REVERT: B 42 ARG cc_start: 0.7598 (ttp-110) cc_final: 0.7107 (ttm-80) REVERT: B 70 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8623 (pt) REVERT: B 100 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8794 (p) REVERT: B 134 ARG cc_start: 0.7350 (ptp-170) cc_final: 0.7117 (ptp-110) REVERT: B 171 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8352 (mm) REVERT: B 186 ASP cc_start: 0.8320 (m-30) cc_final: 0.7627 (m-30) REVERT: B 217 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7760 (pmm) REVERT: G 21 MET cc_start: 0.3696 (tmm) cc_final: 0.3391 (tpt) outliers start: 31 outliers final: 17 residues processed: 156 average time/residue: 1.2372 time to fit residues: 206.5686 Evaluate side-chains 146 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 382 ILE Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 68 optimal weight: 0.8980 chunk 109 optimal weight: 10.0000 chunk 100 optimal weight: 0.2980 chunk 58 optimal weight: 0.9980 chunk 45 optimal weight: 0.0070 chunk 79 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN R 45 GLN B 75 GLN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.192543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.135572 restraints weight = 10089.060| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.60 r_work: 0.3314 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9437 Z= 0.120 Angle : 0.559 7.780 12799 Z= 0.296 Chirality : 0.041 0.189 1412 Planarity : 0.004 0.065 1623 Dihedral : 4.836 45.226 1269 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.95 % Allowed : 22.97 % Favored : 74.09 % 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: 0.14 (0.25), residues: 1133 helix: 1.55 (0.25), residues: 437 sheet: 0.42 (0.33), residues: 234 loop : -1.56 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 33 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.017 0.001 TYR R 148 ARG 0.010 0.000 ARG R 44 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 424) hydrogen bonds : angle 4.18073 ( 1221) SS BOND : bond 0.00109 ( 6) SS BOND : angle 0.88075 ( 12) covalent geometry : bond 0.00273 ( 9431) covalent geometry : angle 0.55899 (12787) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 1.580 Fit side-chains REVERT: A 60 MET cc_start: 0.8198 (mmm) cc_final: 0.7261 (mtt) REVERT: A 272 LEU cc_start: 0.8250 (mt) cc_final: 0.8012 (mp) REVERT: A 308 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7471 (mt) REVERT: A 343 ASP cc_start: 0.7408 (m-30) cc_final: 0.7062 (m-30) REVERT: A 392 GLU cc_start: 0.7849 (mp0) cc_final: 0.7580 (mm-30) REVERT: N 34 MET cc_start: 0.8412 (mmm) cc_final: 0.8004 (mmm) REVERT: N 46 GLU cc_start: 0.8351 (mp0) cc_final: 0.8006 (mp0) REVERT: N 79 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6897 (tp) REVERT: P 3 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6848 (mm-30) REVERT: R 41 GLU cc_start: 0.8419 (pp20) cc_final: 0.7804 (pp20) REVERT: R 44 ARG cc_start: 0.8582 (ttp80) cc_final: 0.8346 (ptp-110) REVERT: R 146 ILE cc_start: 0.8736 (mt) cc_final: 0.8460 (mp) REVERT: R 267 ARG cc_start: 0.7282 (tpt170) cc_final: 0.6259 (mpp80) REVERT: R 336 LYS cc_start: 0.7662 (mttp) cc_final: 0.7342 (mmtm) REVERT: R 348 ARG cc_start: 0.7307 (tpm-80) cc_final: 0.6060 (mtp180) REVERT: R 376 ARG cc_start: 0.7479 (ptp-170) cc_final: 0.6853 (mtt90) REVERT: R 387 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.5898 (mt-10) REVERT: R 418 GLU cc_start: 0.6936 (tp30) cc_final: 0.6624 (tm-30) REVERT: B 42 ARG cc_start: 0.7605 (ttp-110) cc_final: 0.7155 (ttm-80) REVERT: B 70 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8608 (pt) REVERT: B 100 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8790 (p) REVERT: B 134 ARG cc_start: 0.7320 (ptp-170) cc_final: 0.7089 (ptp-110) REVERT: B 171 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8347 (mm) REVERT: B 186 ASP cc_start: 0.8285 (m-30) cc_final: 0.7623 (m-30) REVERT: B 217 MET cc_start: 0.8059 (mpt) cc_final: 0.7751 (pmm) REVERT: G 21 MET cc_start: 0.3631 (tmm) cc_final: 0.3378 (tpt) outliers start: 29 outliers final: 21 residues processed: 145 average time/residue: 1.3668 time to fit residues: 212.5838 Evaluate side-chains 155 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 382 ILE Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 0.7980 chunk 55 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 36 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN G 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.192127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.136417 restraints weight = 10180.113| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.56 r_work: 0.3303 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9437 Z= 0.129 Angle : 0.569 7.769 12799 Z= 0.301 Chirality : 0.041 0.169 1412 Planarity : 0.004 0.065 1623 Dihedral : 4.854 48.357 1269 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.05 % Allowed : 23.17 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.15 (0.25), residues: 1133 helix: 1.53 (0.25), residues: 444 sheet: 0.39 (0.33), residues: 235 loop : -1.53 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP R 33 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE N 108 TYR 0.018 0.001 TYR R 148 ARG 0.015 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 424) hydrogen bonds : angle 4.18339 ( 1221) SS BOND : bond 0.00118 ( 6) SS BOND : angle 0.92103 ( 12) covalent geometry : bond 0.00298 ( 9431) covalent geometry : angle 0.56887 (12787) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 1.073 Fit side-chains REVERT: A 60 MET cc_start: 0.8203 (mmm) cc_final: 0.7317 (mtt) REVERT: A 272 LEU cc_start: 0.8301 (mt) cc_final: 0.8076 (mp) REVERT: A 308 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7628 (tp) REVERT: A 331 ASP cc_start: 0.8052 (t0) cc_final: 0.7690 (t0) REVERT: A 343 ASP cc_start: 0.7344 (m-30) cc_final: 0.6988 (m-30) REVERT: A 392 GLU cc_start: 0.7842 (mp0) cc_final: 0.7592 (mm-30) REVERT: N 34 MET cc_start: 0.8375 (mmm) cc_final: 0.8004 (mmm) REVERT: N 46 GLU cc_start: 0.8351 (mp0) cc_final: 0.8018 (mp0) REVERT: R 41 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7794 (pp20) REVERT: R 146 ILE cc_start: 0.8758 (mt) cc_final: 0.8488 (mp) REVERT: R 267 ARG cc_start: 0.7309 (tpt170) cc_final: 0.6314 (mpp80) REVERT: R 336 LYS cc_start: 0.7711 (mttp) cc_final: 0.7406 (mmtm) REVERT: R 348 ARG cc_start: 0.7345 (tpm-80) cc_final: 0.6116 (mtp180) REVERT: R 387 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.5912 (mt-10) REVERT: R 418 GLU cc_start: 0.6978 (tp30) cc_final: 0.6672 (tm-30) REVERT: B 42 ARG cc_start: 0.7606 (ttp-110) cc_final: 0.7189 (ttm-80) REVERT: B 70 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8650 (pt) REVERT: B 100 VAL cc_start: 0.9018 (OUTLIER) cc_final: 0.8797 (p) REVERT: B 186 ASP cc_start: 0.8304 (m-30) cc_final: 0.7634 (m-30) REVERT: B 217 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7812 (pmm) REVERT: G 21 MET cc_start: 0.3655 (tmm) cc_final: 0.3398 (tpt) outliers start: 30 outliers final: 20 residues processed: 146 average time/residue: 1.2026 time to fit residues: 188.2548 Evaluate side-chains 145 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 41 GLU Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 382 ILE Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN R 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.191677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.134604 restraints weight = 10125.341| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.64 r_work: 0.3309 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9437 Z= 0.137 Angle : 0.577 7.647 12799 Z= 0.305 Chirality : 0.041 0.174 1412 Planarity : 0.005 0.066 1623 Dihedral : 4.899 50.942 1269 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.95 % Allowed : 23.58 % Favored : 73.48 % 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: 0.15 (0.25), residues: 1133 helix: 1.53 (0.25), residues: 444 sheet: 0.38 (0.33), residues: 235 loop : -1.54 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP R 33 HIS 0.004 0.001 HIS A 357 PHE 0.017 0.001 PHE N 108 TYR 0.019 0.001 TYR R 148 ARG 0.014 0.001 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04024 ( 424) hydrogen bonds : angle 4.19543 ( 1221) SS BOND : bond 0.00119 ( 6) SS BOND : angle 0.92425 ( 12) covalent geometry : bond 0.00318 ( 9431) covalent geometry : angle 0.57674 (12787) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7399.95 seconds wall clock time: 131 minutes 42.26 seconds (7902.26 seconds total)