Starting phenix.real_space_refine on Thu Feb 13 18:23:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vbi_31880/02_2025/7vbi_31880.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vbi_31880/02_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_31880/02_2025/7vbi_31880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vbi_31880/02_2025/7vbi_31880.map" model { file = "/net/cci-nas-00/data/ceres_data/7vbi_31880/02_2025/7vbi_31880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vbi_31880/02_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-5592/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: 5.36, per 1000 atoms: 0.58 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: 2.37 Conformation dependent library (CDL) restraints added in 1.0 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: 0.95 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: 2.51 Time building geometry restraints manager: 2.77 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.270 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.590 ------------------------------------------------------------------------------- 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 9431 Z= 0.738 Angle : 1.125 12.808 12787 Z= 0.633 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 *********************** 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 : 0.968 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: 1.3999 time to fit residues: 263.1268 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 : 1.082 ------------------------------------------------------------------------------- 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 = 0.149244 restraints weight = 10073.276| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.74 r_work: 0.3323 rms_B_bonded: 3.22 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 9431 Z= 0.202 Angle : 0.608 8.982 12787 Z= 0.327 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 *********************** 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 : 1.040 Fit side-chains REVERT: A 272 LEU cc_start: 0.8367 (mt) cc_final: 0.8115 (mm) REVERT: A 283 ARG cc_start: 0.7823 (ptp-110) cc_final: 0.7535 (mtm110) REVERT: A 347 ARG cc_start: 0.7811 (ttp-170) cc_final: 0.7583 (ttp80) REVERT: N 34 MET cc_start: 0.8464 (mmm) cc_final: 0.8073 (mmm) REVERT: N 39 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: N 46 GLU cc_start: 0.8183 (mp0) cc_final: 0.7944 (mp0) REVERT: P 3 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7107 (mm-30) REVERT: R 146 ILE cc_start: 0.8806 (mt) cc_final: 0.8581 (mp) REVERT: R 167 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7670 (pp) REVERT: R 202 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7463 (tttp) REVERT: R 267 ARG cc_start: 0.7290 (tpt170) cc_final: 0.6351 (mpp80) REVERT: R 336 LYS cc_start: 0.7865 (mttp) cc_final: 0.7598 (mmtm) REVERT: R 376 ARG cc_start: 0.7732 (ptp-170) cc_final: 0.6998 (mtt90) REVERT: R 387 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.5830 (mt-10) REVERT: B 42 ARG cc_start: 0.7283 (ttp-110) cc_final: 0.6769 (ttm-80) REVERT: B 217 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7844 (pmm) REVERT: G 21 MET cc_start: 0.5284 (OUTLIER) cc_final: 0.4988 (tmm) outliers start: 37 outliers final: 14 residues processed: 165 average time/residue: 1.3729 time to fit residues: 241.0384 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 : 1.077 ------------------------------------------------------------------------------- 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: 0.7980 chunk 63 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 86 optimal weight: 0.0370 chunk 2 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 85 optimal weight: 0.0070 overall best weight: 0.7680 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 HIS N 31 ASN N 77 ASN R 37 GLN R 47 GLN B 230 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.192908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.148961 restraints weight = 10265.510| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.72 r_work: 0.3346 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 9431 Z= 0.217 Angle : 0.588 8.008 12787 Z= 0.313 Chirality : 0.041 0.161 1412 Planarity : 0.004 0.062 1623 Dihedral : 5.449 39.357 1269 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.27 % Allowed : 14.53 % Favored : 81.20 % 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: -1.11 (0.24), residues: 1133 helix: 0.36 (0.25), residues: 433 sheet: -0.43 (0.32), residues: 242 loop : -1.97 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 214 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.020 0.001 TYR R 148 ARG 0.009 0.000 ARG R 44 *********************** 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 189 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 LEU cc_start: 0.8322 (mt) cc_final: 0.8092 (mp) REVERT: A 283 ARG cc_start: 0.7880 (ptp-110) cc_final: 0.7624 (mtm110) REVERT: A 308 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7756 (tp) REVERT: A 386 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8149 (ttm) REVERT: N 34 MET cc_start: 0.8425 (mmm) cc_final: 0.8084 (mmm) REVERT: N 39 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: N 46 GLU cc_start: 0.8280 (mp0) cc_final: 0.7976 (mp0) REVERT: P 3 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7082 (mm-30) REVERT: R 44 ARG cc_start: 0.8461 (ttp80) cc_final: 0.8177 (ttp80) REVERT: R 146 ILE cc_start: 0.8802 (mt) cc_final: 0.8584 (mp) REVERT: R 202 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7459 (tptp) REVERT: R 267 ARG cc_start: 0.7248 (tpt170) cc_final: 0.6353 (mpp80) REVERT: R 336 LYS cc_start: 0.7787 (mttp) cc_final: 0.7454 (mmtm) REVERT: R 348 ARG cc_start: 0.7388 (tpm-80) cc_final: 0.6241 (mtp180) REVERT: R 365 VAL cc_start: 0.7726 (OUTLIER) cc_final: 0.7492 (p) REVERT: R 376 ARG cc_start: 0.7673 (ptp-170) cc_final: 0.7020 (mtt90) REVERT: R 387 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.5947 (mt-10) REVERT: B 42 ARG cc_start: 0.7469 (ttp-110) cc_final: 0.6970 (ttm-80) REVERT: B 70 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8675 (pt) REVERT: B 171 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8335 (mm) REVERT: B 217 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7796 (pmm) REVERT: G 21 MET cc_start: 0.5286 (OUTLIER) cc_final: 0.4955 (tmm) outliers start: 42 outliers final: 16 residues processed: 171 average time/residue: 1.2477 time to fit residues: 228.0800 Evaluate side-chains 154 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 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 194 VAL Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 365 VAL 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 294 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 53 optimal weight: 0.9980 chunk 99 optimal weight: 0.0170 chunk 90 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 43 optimal weight: 50.0000 overall best weight: 1.4022 ------------------------------------------------------------------------------- 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 R 394 GLN B 75 GLN B 230 ASN B 239 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.189235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.132057 restraints weight = 10157.829| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.55 r_work: 0.3258 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9431 Z= 0.306 Angle : 0.614 8.018 12787 Z= 0.327 Chirality : 0.043 0.156 1412 Planarity : 0.005 0.062 1623 Dihedral : 5.336 36.357 1269 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.27 % Allowed : 17.28 % Favored : 78.46 % 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: -0.77 (0.24), residues: 1133 helix: 0.71 (0.25), residues: 430 sheet: -0.11 (0.33), residues: 229 loop : -1.88 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 214 HIS 0.006 0.001 HIS A 357 PHE 0.019 0.002 PHE N 108 TYR 0.023 0.002 TYR R 148 ARG 0.005 0.000 ARG A 356 *********************** 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 183 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 141 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 LEU cc_start: 0.8214 (mt) cc_final: 0.7968 (mp) REVERT: A 283 ARG cc_start: 0.7766 (ptp-110) cc_final: 0.7479 (mtm110) REVERT: A 308 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7686 (tp) REVERT: A 386 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8115 (ttm) REVERT: N 34 MET cc_start: 0.8431 (mmm) cc_final: 0.8089 (mmm) REVERT: N 39 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8070 (tt0) REVERT: N 46 GLU cc_start: 0.8307 (mp0) cc_final: 0.8044 (mp0) REVERT: P 3 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6774 (mm-30) REVERT: R 146 ILE cc_start: 0.8797 (mt) cc_final: 0.8542 (mp) REVERT: R 202 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7390 (tttp) REVERT: R 267 ARG cc_start: 0.7240 (tpt170) cc_final: 0.6218 (mpp80) REVERT: R 303 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8072 (mtt) REVERT: R 336 LYS cc_start: 0.7734 (mttp) cc_final: 0.7335 (mmtm) REVERT: R 348 ARG cc_start: 0.7396 (tpm-80) cc_final: 0.6160 (mtp180) REVERT: R 364 GLU cc_start: 0.7754 (mp0) cc_final: 0.7495 (mp0) REVERT: R 376 ARG cc_start: 0.7719 (ptp-170) cc_final: 0.7050 (mmt90) REVERT: R 387 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.5944 (mt-10) REVERT: B 42 ARG cc_start: 0.7608 (ttp-110) cc_final: 0.7125 (ttm-80) REVERT: B 70 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8760 (pt) REVERT: B 100 VAL cc_start: 0.9149 (OUTLIER) cc_final: 0.8887 (p) REVERT: B 171 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8400 (mm) REVERT: B 217 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7686 (pmm) REVERT: B 239 ASN cc_start: 0.7542 (m-40) cc_final: 0.7341 (m110) REVERT: G 21 MET cc_start: 0.5051 (OUTLIER) cc_final: 0.4745 (tmm) outliers start: 42 outliers final: 16 residues processed: 169 average time/residue: 1.2708 time to fit residues: 228.9388 Evaluate side-chains 151 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 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 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 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 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 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: 1.9990 chunk 70 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 82 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.191774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.137362 restraints weight = 10199.400| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.42 r_work: 0.3295 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9431 Z= 0.209 Angle : 0.572 8.768 12787 Z= 0.302 Chirality : 0.041 0.155 1412 Planarity : 0.004 0.063 1623 Dihedral : 5.123 36.571 1269 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.96 % Allowed : 19.00 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.24), residues: 1133 helix: 1.01 (0.25), residues: 438 sheet: 0.04 (0.33), residues: 234 loop : -1.79 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 214 HIS 0.004 0.001 HIS A 357 PHE 0.018 0.001 PHE N 108 TYR 0.019 0.001 TYR N 95 ARG 0.008 0.000 ARG R 44 *********************** 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 173 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.998 Fit side-chains REVERT: A 272 LEU cc_start: 0.8346 (mt) cc_final: 0.8133 (mp) REVERT: A 283 ARG cc_start: 0.7787 (ptp-110) cc_final: 0.7414 (mtm110) REVERT: A 308 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7540 (mt) REVERT: A 386 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8222 (ttm) REVERT: N 34 MET cc_start: 0.8367 (mmm) cc_final: 0.8075 (mmm) REVERT: N 39 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.8025 (tt0) REVERT: N 46 GLU cc_start: 0.8399 (mp0) cc_final: 0.8171 (mp0) REVERT: P 3 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6926 (mm-30) REVERT: R 37 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7531 (mm110) REVERT: R 44 ARG cc_start: 0.8482 (ttp80) cc_final: 0.8089 (ttp80) REVERT: R 146 ILE cc_start: 0.8794 (mt) cc_final: 0.8560 (mp) REVERT: R 202 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7475 (tttp) REVERT: R 267 ARG cc_start: 0.7325 (tpt170) cc_final: 0.6346 (mpp80) REVERT: R 303 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7972 (mtt) REVERT: R 336 LYS cc_start: 0.7743 (mttp) cc_final: 0.7432 (mmtm) REVERT: R 348 ARG cc_start: 0.7433 (tpm-80) cc_final: 0.6241 (mtp180) REVERT: R 376 ARG cc_start: 0.7558 (ptp-170) cc_final: 0.6929 (mtt90) REVERT: R 387 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6086 (mt-10) REVERT: B 42 ARG cc_start: 0.7625 (ttp-110) cc_final: 0.7365 (tpt170) REVERT: B 70 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8691 (pt) REVERT: B 100 VAL cc_start: 0.9077 (OUTLIER) cc_final: 0.8865 (p) REVERT: B 217 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7764 (pmm) REVERT: G 21 MET cc_start: 0.5126 (OUTLIER) cc_final: 0.4847 (tmm) outliers start: 39 outliers final: 17 residues processed: 157 average time/residue: 1.3117 time to fit residues: 221.8485 Evaluate side-chains 159 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 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 105 THR Chi-restraints excluded: chain R residue 194 VAL 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 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: 0.0070 chunk 62 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 47 optimal weight: 0.5980 chunk 26 optimal weight: 0.0470 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN B 75 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 = 0.4170 r_free = 0.4170 target = 0.193144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.147649 restraints weight = 9992.202| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.85 r_work: 0.3339 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9431 Z= 0.157 Angle : 0.543 7.847 12787 Z= 0.289 Chirality : 0.040 0.158 1412 Planarity : 0.004 0.065 1623 Dihedral : 4.890 35.935 1269 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.76 % Allowed : 20.33 % Favored : 75.91 % 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: 1.31 (0.25), residues: 438 sheet: 0.26 (0.33), residues: 234 loop : -1.70 (0.27), residues: 461 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 0.017 0.001 PHE B 292 TYR 0.022 0.001 TYR A 311 ARG 0.009 0.000 ARG A 356 *********************** 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 182 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 1.024 Fit side-chains REVERT: A 272 LEU cc_start: 0.8298 (mt) cc_final: 0.8066 (mp) REVERT: A 283 ARG cc_start: 0.7730 (ptp-110) cc_final: 0.7430 (mtm110) REVERT: A 308 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7504 (mt) REVERT: A 331 ASP cc_start: 0.8106 (t0) cc_final: 0.7651 (t0) REVERT: A 343 ASP cc_start: 0.7346 (m-30) cc_final: 0.6992 (m-30) REVERT: A 392 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7667 (mm-30) REVERT: N 34 MET cc_start: 0.8357 (mmm) cc_final: 0.8037 (mmm) REVERT: N 46 GLU cc_start: 0.8399 (mp0) cc_final: 0.8157 (mp0) REVERT: P 3 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6890 (mm-30) REVERT: R 41 GLU cc_start: 0.8435 (pp20) cc_final: 0.7979 (pp20) REVERT: R 44 ARG cc_start: 0.8341 (ttp80) cc_final: 0.8091 (ptp-110) REVERT: R 68 GLU cc_start: 0.5378 (tt0) cc_final: 0.5072 (tt0) REVERT: R 109 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8179 (mm) REVERT: R 146 ILE cc_start: 0.8762 (mt) cc_final: 0.8496 (mp) REVERT: R 202 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7461 (tptp) REVERT: R 267 ARG cc_start: 0.7348 (tpt170) cc_final: 0.6400 (mpp80) REVERT: R 294 GLU cc_start: 0.7068 (mm-30) cc_final: 0.6591 (pp20) REVERT: R 336 LYS cc_start: 0.7737 (mttp) cc_final: 0.7433 (mmtm) REVERT: R 348 ARG cc_start: 0.7390 (tpm-80) cc_final: 0.6216 (mtp180) REVERT: R 376 ARG cc_start: 0.7560 (ptp-170) cc_final: 0.6926 (mmt90) REVERT: R 383 LYS cc_start: 0.8480 (tttt) cc_final: 0.8271 (tttp) REVERT: R 387 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.5955 (mt-10) REVERT: R 418 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6962 (tm-30) REVERT: B 70 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8610 (pt) REVERT: B 123 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8671 (mm) REVERT: B 186 ASP cc_start: 0.8317 (m-30) cc_final: 0.7691 (m-30) REVERT: B 217 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7802 (pmm) REVERT: G 21 MET cc_start: 0.4896 (OUTLIER) cc_final: 0.4676 (tmm) outliers start: 37 outliers final: 16 residues processed: 169 average time/residue: 1.1978 time to fit residues: 216.8966 Evaluate side-chains 151 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 A residue 392 GLU 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 109 LEU Chi-restraints excluded: chain R residue 194 VAL 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 70 LEU Chi-restraints excluded: chain B residue 123 ILE 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 Chi-restraints excluded: chain G residue 21 MET 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: 10.0000 chunk 76 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4148 r_free = 0.4148 target = 0.190928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.136840 restraints weight = 10215.052| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.57 r_work: 0.3297 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9431 Z= 0.283 Angle : 0.597 7.797 12787 Z= 0.316 Chirality : 0.042 0.160 1412 Planarity : 0.004 0.065 1623 Dihedral : 5.072 38.342 1269 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.47 % Allowed : 20.53 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.25), residues: 1133 helix: 1.28 (0.25), residues: 433 sheet: 0.21 (0.33), residues: 234 loop : -1.65 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.020 0.002 PHE N 108 TYR 0.021 0.002 TYR R 148 ARG 0.014 0.000 ARG B 197 *********************** 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 170 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 126 time to evaluate : 1.006 Fit side-chains REVERT: A 272 LEU cc_start: 0.8373 (mt) cc_final: 0.8167 (mp) REVERT: A 283 ARG cc_start: 0.7774 (ptp-110) cc_final: 0.7459 (mtm110) REVERT: A 308 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7759 (tp) REVERT: A 392 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7696 (mm-30) REVERT: N 34 MET cc_start: 0.8356 (mmm) cc_final: 0.8042 (mmm) REVERT: N 46 GLU cc_start: 0.8390 (mp0) cc_final: 0.8108 (mp0) REVERT: P 3 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6887 (mm-30) REVERT: R 41 GLU cc_start: 0.8389 (pp20) cc_final: 0.7800 (pp20) REVERT: R 146 ILE cc_start: 0.8789 (mt) cc_final: 0.8528 (mp) REVERT: R 202 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7475 (tttp) REVERT: R 267 ARG cc_start: 0.7305 (tpt170) cc_final: 0.6355 (mpp80) REVERT: R 336 LYS cc_start: 0.7771 (mttp) cc_final: 0.7399 (mmtm) REVERT: R 348 ARG cc_start: 0.7434 (tpm-80) cc_final: 0.6219 (mtp180) REVERT: R 376 ARG cc_start: 0.7470 (ptp-170) cc_final: 0.6836 (mmt90) REVERT: R 387 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6106 (mt-10) REVERT: R 418 GLU cc_start: 0.7320 (mm-30) cc_final: 0.7049 (tm-30) REVERT: B 70 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8760 (pt) REVERT: B 171 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8355 (mm) REVERT: B 217 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7843 (pmm) outliers start: 44 outliers final: 19 residues processed: 154 average time/residue: 1.2572 time to fit residues: 206.9147 Evaluate side-chains 154 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 A residue 392 GLU 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 29 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.191955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.137687 restraints weight = 10319.918| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.47 r_work: 0.3315 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9431 Z= 0.213 Angle : 0.575 7.922 12787 Z= 0.304 Chirality : 0.041 0.173 1412 Planarity : 0.004 0.065 1623 Dihedral : 5.002 40.099 1269 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.96 % Allowed : 21.54 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.25), residues: 1133 helix: 1.34 (0.25), residues: 439 sheet: 0.20 (0.33), residues: 236 loop : -1.62 (0.27), residues: 458 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 0.018 0.001 PHE N 108 TYR 0.019 0.001 TYR A 311 ARG 0.010 0.000 ARG B 197 *********************** 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 170 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 1.081 Fit side-chains REVERT: A 272 LEU cc_start: 0.8344 (mt) cc_final: 0.8140 (mp) REVERT: A 283 ARG cc_start: 0.7752 (ptp-110) cc_final: 0.7443 (mtm110) REVERT: A 308 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7663 (tp) REVERT: A 331 ASP cc_start: 0.8103 (t0) cc_final: 0.7647 (t0) REVERT: A 343 ASP cc_start: 0.7370 (m-30) cc_final: 0.7021 (m-30) REVERT: A 386 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8276 (ttm) REVERT: A 392 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7681 (mm-30) REVERT: N 34 MET cc_start: 0.8354 (mmm) cc_final: 0.8044 (mmm) REVERT: N 39 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.8007 (tt0) REVERT: N 46 GLU cc_start: 0.8391 (mp0) cc_final: 0.8102 (mp0) REVERT: P 3 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6930 (mm-30) REVERT: R 41 GLU cc_start: 0.8393 (pp20) cc_final: 0.7938 (pp20) REVERT: R 146 ILE cc_start: 0.8779 (mt) cc_final: 0.8520 (mp) REVERT: R 202 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7469 (tttp) REVERT: R 267 ARG cc_start: 0.7323 (tpt170) cc_final: 0.6409 (mpp80) REVERT: R 336 LYS cc_start: 0.7767 (mttp) cc_final: 0.7480 (mmtm) REVERT: R 348 ARG cc_start: 0.7416 (tpm-80) cc_final: 0.6213 (mtp180) REVERT: R 376 ARG cc_start: 0.7461 (ptp-170) cc_final: 0.6829 (mmt90) REVERT: R 383 LYS cc_start: 0.8499 (tttt) cc_final: 0.8269 (tttp) REVERT: R 387 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6019 (mt-10) REVERT: R 418 GLU cc_start: 0.7313 (mm-30) cc_final: 0.7041 (tm-30) REVERT: B 70 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8690 (pt) REVERT: B 171 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8369 (mm) REVERT: B 186 ASP cc_start: 0.8399 (m-30) cc_final: 0.7709 (m-30) REVERT: B 217 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7847 (pmm) REVERT: G 21 MET cc_start: 0.3911 (tmm) cc_final: 0.3575 (tpt) outliers start: 39 outliers final: 21 residues processed: 154 average time/residue: 1.2150 time to fit residues: 200.4437 Evaluate side-chains 152 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 A residue 386 MET Chi-restraints excluded: chain A residue 392 GLU 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 72 TRP Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 174 CYS 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 70 LEU Chi-restraints excluded: chain B residue 133 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 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: 0.0020 chunk 109 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 42 optimal weight: 0.0170 overall best weight: 0.7628 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.192346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.138629 restraints weight = 10130.457| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.57 r_work: 0.3339 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9431 Z= 0.206 Angle : 0.569 7.417 12787 Z= 0.300 Chirality : 0.041 0.166 1412 Planarity : 0.005 0.065 1623 Dihedral : 4.957 43.451 1269 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.05 % Allowed : 22.26 % Favored : 74.70 % 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: -0.01 (0.25), residues: 1133 helix: 1.41 (0.25), residues: 444 sheet: 0.22 (0.33), residues: 236 loop : -1.61 (0.27), residues: 453 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 0.016 0.001 PHE N 108 TYR 0.018 0.001 TYR R 148 ARG 0.013 0.001 ARG B 134 *********************** 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 156 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 1.045 Fit side-chains REVERT: A 272 LEU cc_start: 0.8261 (mt) cc_final: 0.8030 (mp) REVERT: A 283 ARG cc_start: 0.7686 (ptp-110) cc_final: 0.7383 (mtm110) REVERT: A 308 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7642 (tp) REVERT: A 343 ASP cc_start: 0.7336 (m-30) cc_final: 0.6953 (m-30) REVERT: A 386 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8212 (ttm) REVERT: A 392 GLU cc_start: 0.7888 (mp0) cc_final: 0.7616 (mm-30) REVERT: N 34 MET cc_start: 0.8361 (mmm) cc_final: 0.8044 (mmm) REVERT: N 39 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7996 (tt0) REVERT: N 46 GLU cc_start: 0.8374 (mp0) cc_final: 0.8063 (mp0) REVERT: P 3 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6788 (mm-30) REVERT: R 41 GLU cc_start: 0.8424 (pp20) cc_final: 0.7927 (pp20) REVERT: R 146 ILE cc_start: 0.8746 (mt) cc_final: 0.8475 (mp) REVERT: R 202 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7418 (tttp) REVERT: R 233 MET cc_start: 0.8300 (tmm) cc_final: 0.7984 (ttt) REVERT: R 267 ARG cc_start: 0.7329 (tpt170) cc_final: 0.6353 (mpp80) REVERT: R 336 LYS cc_start: 0.7707 (mttp) cc_final: 0.7402 (mmtm) REVERT: R 348 ARG cc_start: 0.7363 (tpm-80) cc_final: 0.6135 (mtp180) REVERT: R 376 ARG cc_start: 0.7426 (ptp-170) cc_final: 0.6786 (mmt90) REVERT: R 383 LYS cc_start: 0.8431 (tttt) cc_final: 0.8201 (tttp) REVERT: R 387 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.5944 (mt-10) REVERT: R 418 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6981 (tm-30) REVERT: B 70 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8659 (pt) REVERT: B 171 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8361 (mm) REVERT: B 186 ASP cc_start: 0.8369 (m-30) cc_final: 0.7704 (m-30) REVERT: B 217 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7799 (pmm) REVERT: G 21 MET cc_start: 0.3742 (tmm) cc_final: 0.3457 (tpt) outliers start: 30 outliers final: 19 residues processed: 144 average time/residue: 1.3063 time to fit residues: 200.6882 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 : 1.170 ------------------------------------------------------------------------------- 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 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 72 TRP Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 174 CYS 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 70 LEU Chi-restraints excluded: chain B residue 133 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 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: 1.9990 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.190769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.135406 restraints weight = 10215.554| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.54 r_work: 0.3272 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9431 Z= 0.272 Angle : 0.609 7.613 12787 Z= 0.321 Chirality : 0.042 0.180 1412 Planarity : 0.005 0.065 1623 Dihedral : 5.089 49.616 1269 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.05 % Allowed : 22.76 % Favored : 74.19 % 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: -0.04 (0.25), residues: 1133 helix: 1.37 (0.25), residues: 445 sheet: 0.16 (0.33), residues: 237 loop : -1.58 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.020 0.002 PHE N 108 TYR 0.021 0.001 TYR R 148 ARG 0.015 0.001 ARG B 197 ********************** 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 160 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 1.043 Fit side-chains REVERT: A 60 MET cc_start: 0.8220 (mmm) cc_final: 0.7312 (mtt) REVERT: A 272 LEU cc_start: 0.8375 (mt) cc_final: 0.8173 (mp) REVERT: A 283 ARG cc_start: 0.7767 (ptp-110) cc_final: 0.7460 (mtm110) REVERT: A 308 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7694 (tp) REVERT: A 331 ASP cc_start: 0.8120 (t0) cc_final: 0.7650 (t0) REVERT: A 386 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8356 (ttm) REVERT: A 392 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7705 (mm-30) REVERT: N 34 MET cc_start: 0.8413 (mmm) cc_final: 0.8090 (mmm) REVERT: N 39 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.8057 (tt0) REVERT: N 46 GLU cc_start: 0.8444 (mp0) cc_final: 0.8147 (mp0) REVERT: R 41 GLU cc_start: 0.8426 (pp20) cc_final: 0.7820 (pp20) REVERT: R 146 ILE cc_start: 0.8816 (mt) cc_final: 0.8561 (mp) REVERT: R 202 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7489 (tttp) REVERT: R 233 MET cc_start: 0.8408 (tmm) cc_final: 0.8104 (ttt) REVERT: R 267 ARG cc_start: 0.7286 (tpt170) cc_final: 0.6322 (mpp80) REVERT: R 336 LYS cc_start: 0.7809 (mttp) cc_final: 0.7489 (mmtm) REVERT: R 348 ARG cc_start: 0.7444 (tpm-80) cc_final: 0.6211 (mtp180) REVERT: R 376 ARG cc_start: 0.7484 (ptp-170) cc_final: 0.6855 (mtt90) REVERT: R 383 LYS cc_start: 0.8504 (tttt) cc_final: 0.8261 (tttp) REVERT: R 387 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6154 (mt-10) REVERT: R 418 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7034 (tm-30) REVERT: B 70 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8754 (pt) REVERT: B 171 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8394 (mm) REVERT: B 217 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7856 (pmm) REVERT: G 21 MET cc_start: 0.3684 (tmm) cc_final: 0.3437 (tpt) outliers start: 30 outliers final: 20 residues processed: 147 average time/residue: 1.2359 time to fit residues: 194.6397 Evaluate side-chains 148 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 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 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 A residue 386 MET Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 91 THR 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 174 CYS 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 70 LEU Chi-restraints excluded: chain B residue 133 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 50.0000 chunk 82 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.191874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.139105 restraints weight = 10137.829| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.48 r_work: 0.3319 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9431 Z= 0.230 Angle : 0.603 7.638 12787 Z= 0.318 Chirality : 0.042 0.171 1412 Planarity : 0.005 0.067 1623 Dihedral : 5.188 50.843 1269 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.15 % Allowed : 22.66 % Favored : 74.19 % 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: 0.02 (0.25), residues: 1133 helix: 1.45 (0.25), residues: 444 sheet: 0.22 (0.33), residues: 236 loop : -1.59 (0.27), residues: 453 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 0.015 0.001 PHE B 235 TYR 0.030 0.002 TYR A 311 ARG 0.015 0.001 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6584.15 seconds wall clock time: 116 minutes 51.45 seconds (7011.45 seconds total)