Starting phenix.real_space_refine on Wed Sep 17 13:38:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eq1_31254/09_2025/7eq1_31254.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eq1_31254/09_2025/7eq1_31254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7eq1_31254/09_2025/7eq1_31254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eq1_31254/09_2025/7eq1_31254.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7eq1_31254/09_2025/7eq1_31254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eq1_31254/09_2025/7eq1_31254.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 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 56 5.16 5 C 5728 2.51 5 N 1546 2.21 5 O 1669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8999 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1959 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2212 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 272} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "S" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1787 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "B" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2596 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 2.20, per 1000 atoms: 0.24 Number of scatterers: 8999 At special positions: 0 Unit cell: (115.56, 117.72, 105.84, 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 56 16.00 O 1669 8.00 N 1546 7.00 C 5728 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 314 " - pdb=" SG CYS R 404 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 369.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 35.0% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 6 through 40 removed outlier: 3.574A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.543A pdb=" N LYS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.654A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.673A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.200A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.996A 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 352 removed outlier: 3.642A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 389 removed outlier: 3.935A pdb=" N ILE A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'R' and resid 228 through 233 removed outlier: 3.625A pdb=" N VAL R 231 " --> pdb=" O TYR R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 244 through 273 removed outlier: 3.645A pdb=" N CYS R 256 " --> pdb=" O SER R 252 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU R 264 " --> pdb=" O ILE R 260 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE R 271 " --> pdb=" O VAL R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 299 removed outlier: 3.722A pdb=" N LEU R 299 " --> pdb=" O ASN R 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 304 removed outlier: 4.104A pdb=" N ALA R 303 " --> pdb=" O LEU R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 312 through 344 removed outlier: 4.228A pdb=" N ALA R 316 " --> pdb=" O SER R 312 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU R 317 " --> pdb=" O ALA R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 353 through 364 removed outlier: 3.570A pdb=" N LEU R 361 " --> pdb=" O LYS R 357 " (cutoff:3.500A) Processing helix chain 'R' and resid 370 through 376 removed outlier: 4.107A pdb=" N SER R 375 " --> pdb=" O LEU R 371 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL R 376 " --> pdb=" O LEU R 372 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 442 removed outlier: 3.581A pdb=" N LEU R 425 " --> pdb=" O GLY R 421 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE R 426 " --> pdb=" O LEU R 422 " (cutoff:3.500A) Processing helix chain 'R' and resid 456 through 467 Processing helix chain 'R' and resid 468 through 473 removed outlier: 3.539A pdb=" N ALA R 473 " --> pdb=" O TRP R 470 " (cutoff:3.500A) Processing helix chain 'R' and resid 480 through 493 removed outlier: 3.640A pdb=" N GLN R 484 " --> pdb=" O PHE R 480 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE R 488 " --> pdb=" O GLN R 484 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR R 489 " --> pdb=" O LEU R 485 " (cutoff:3.500A) Processing helix chain 'R' and resid 494 through 520 Processing helix chain 'S' and resid 62 through 65 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.612A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.505A pdb=" N ASP S 223 " --> pdb=" O GLU S 220 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 220 through 224' Processing helix chain 'Y' and resid 7 through 24 removed outlier: 3.687A pdb=" N GLN Y 11 " --> pdb=" O ALA Y 7 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS Y 14 " --> pdb=" O ALA Y 10 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU Y 15 " --> pdb=" O GLN Y 11 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL Y 16 " --> pdb=" O ALA Y 12 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU Y 17 " --> pdb=" O ARG Y 13 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 44 Processing helix chain 'B' and resid 5 through 26 removed outlier: 3.820A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.900A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.900A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.869A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AA6, first strand: chain 'S' and resid 147 through 148 removed outlier: 3.738A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.720A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.696A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.065A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.582A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.928A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.221A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.716A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2917 1.34 - 1.46: 2146 1.46 - 1.58: 4053 1.58 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 9197 Sorted by residual: bond pdb=" CB MET S 230 " pdb=" CG MET S 230 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 8.31e-01 bond pdb=" CG MET B 61 " pdb=" SD MET B 61 " ideal model delta sigma weight residual 1.803 1.782 0.021 2.50e-02 1.60e+03 6.85e-01 bond pdb=" CB PRO S 236 " pdb=" CG PRO S 236 " ideal model delta sigma weight residual 1.506 1.475 0.031 3.90e-02 6.57e+02 6.50e-01 bond pdb=" CB ILE S 58 " pdb=" CG2 ILE S 58 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.25e-01 bond pdb=" CB ARG S 98 " pdb=" CG ARG S 98 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.24e-01 ... (remaining 9192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 12200 1.68 - 3.35: 227 3.35 - 5.03: 39 5.03 - 6.71: 8 6.71 - 8.38: 1 Bond angle restraints: 12475 Sorted by residual: angle pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta sigma weight residual 121.54 129.92 -8.38 1.91e+00 2.74e-01 1.93e+01 angle pdb=" CA CYS R 404 " pdb=" CB CYS R 404 " pdb=" SG CYS R 404 " ideal model delta sigma weight residual 114.40 120.30 -5.90 2.30e+00 1.89e-01 6.58e+00 angle pdb=" C VAL A 367 " pdb=" N ASP A 368 " pdb=" CA ASP A 368 " ideal model delta sigma weight residual 121.54 126.39 -4.85 1.91e+00 2.74e-01 6.45e+00 angle pdb=" C PRO R 241 " pdb=" N ALA R 242 " pdb=" CA ALA R 242 " ideal model delta sigma weight residual 121.54 126.21 -4.67 1.91e+00 2.74e-01 5.98e+00 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 121.54 126.02 -4.48 1.91e+00 2.74e-01 5.49e+00 ... (remaining 12470 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4922 17.97 - 35.94: 420 35.94 - 53.91: 71 53.91 - 71.88: 10 71.88 - 89.84: 9 Dihedral angle restraints: 5432 sinusoidal: 2100 harmonic: 3332 Sorted by residual: dihedral pdb=" CB CYS R 314 " pdb=" SG CYS R 314 " pdb=" SG CYS R 404 " pdb=" CB CYS R 404 " ideal model delta sinusoidal sigma weight residual -86.00 -158.88 72.88 1 1.00e+01 1.00e-02 6.77e+01 dihedral pdb=" CA LEU R 235 " pdb=" C LEU R 235 " pdb=" N SER R 236 " pdb=" CA SER R 236 " ideal model delta harmonic sigma weight residual 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA VAL B 213 " pdb=" C VAL B 213 " pdb=" N ARG B 214 " pdb=" CA ARG B 214 " ideal model delta harmonic sigma weight residual 180.00 161.71 18.29 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 5429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 831 0.031 - 0.062: 391 0.062 - 0.093: 125 0.093 - 0.124: 54 0.124 - 0.155: 10 Chirality restraints: 1411 Sorted by residual: chirality pdb=" CB ILE R 386 " pdb=" CA ILE R 386 " pdb=" CG1 ILE R 386 " pdb=" CG2 ILE R 386 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CB THR S 91 " pdb=" CA THR S 91 " pdb=" OG1 THR S 91 " pdb=" CG2 THR S 91 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA VAL R 240 " pdb=" N VAL R 240 " pdb=" C VAL R 240 " pdb=" CB VAL R 240 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 1408 not shown) Planarity restraints: 1581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.015 2.00e-02 2.50e+03 1.22e-02 2.97e+00 pdb=" CG TYR B 59 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE S 239 " 0.012 2.00e-02 2.50e+03 1.25e-02 2.75e+00 pdb=" CG PHE S 239 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE S 239 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE S 239 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE S 239 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE S 239 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE S 239 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 309 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO R 310 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO R 310 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 310 " -0.021 5.00e-02 4.00e+02 ... (remaining 1578 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 156 2.67 - 3.23: 8576 3.23 - 3.78: 14129 3.78 - 4.34: 19172 4.34 - 4.90: 31434 Nonbonded interactions: 73467 Sorted by model distance: nonbonded pdb=" OG1 THR B 184 " pdb=" OD2 ASP B 205 " model vdw 2.113 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.129 3.040 nonbonded pdb=" OD2 ASP Y 48 " pdb=" OG SER B 281 " model vdw 2.144 3.040 nonbonded pdb=" O PHE A 376 " pdb=" OH TYR R 347 " model vdw 2.180 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.202 3.040 ... (remaining 73462 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.010 Find NCS groups from input model: 0.040 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:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9199 Z= 0.146 Angle : 0.584 8.383 12479 Z= 0.310 Chirality : 0.042 0.155 1411 Planarity : 0.004 0.040 1581 Dihedral : 13.831 89.845 3278 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.26), residues: 1134 helix: 0.75 (0.29), residues: 363 sheet: -0.43 (0.30), residues: 282 loop : -1.18 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 283 TYR 0.030 0.002 TYR B 59 PHE 0.028 0.002 PHE S 239 TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9197) covalent geometry : angle 0.58421 (12475) SS BOND : bond 0.00690 ( 2) SS BOND : angle 1.11973 ( 4) hydrogen bonds : bond 0.15904 ( 401) hydrogen bonds : angle 6.71385 ( 1167) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.338 Fit side-chains REVERT: A 9 ASP cc_start: 0.7432 (m-30) cc_final: 0.7182 (m-30) REVERT: A 207 ILE cc_start: 0.8337 (mm) cc_final: 0.8119 (mm) REVERT: A 327 GLU cc_start: 0.7680 (mp0) cc_final: 0.7364 (mp0) REVERT: R 361 LEU cc_start: 0.8508 (tp) cc_final: 0.8182 (tp) REVERT: R 485 LEU cc_start: 0.7710 (mt) cc_final: 0.7486 (mm) REVERT: R 492 ASN cc_start: 0.8280 (m-40) cc_final: 0.7836 (m-40) REVERT: S 192 MET cc_start: 0.7267 (ptt) cc_final: 0.7067 (ptt) REVERT: B 27 ASP cc_start: 0.7392 (p0) cc_final: 0.7073 (p0) REVERT: B 37 ILE cc_start: 0.8616 (mm) cc_final: 0.8406 (mm) REVERT: B 44 GLN cc_start: 0.6858 (mp-120) cc_final: 0.5873 (mp-120) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1135 time to fit residues: 29.6025 Evaluate side-chains 184 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN R 454 HIS B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.131793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.113251 restraints weight = 12855.975| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.97 r_work: 0.3272 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9199 Z= 0.155 Angle : 0.582 7.049 12479 Z= 0.305 Chirality : 0.043 0.174 1411 Planarity : 0.004 0.041 1581 Dihedral : 4.604 21.000 1251 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.74 % Allowed : 8.92 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.26), residues: 1134 helix: 0.74 (0.29), residues: 374 sheet: -0.21 (0.30), residues: 284 loop : -1.24 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 42 TYR 0.016 0.001 TYR A 391 PHE 0.026 0.002 PHE S 68 TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9197) covalent geometry : angle 0.58133 (12475) SS BOND : bond 0.00622 ( 2) SS BOND : angle 1.51571 ( 4) hydrogen bonds : bond 0.04115 ( 401) hydrogen bonds : angle 4.88109 ( 1167) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6962 (mt-10) REVERT: A 207 ILE cc_start: 0.8512 (mm) cc_final: 0.8184 (mm) REVERT: A 293 LYS cc_start: 0.8218 (mtmt) cc_final: 0.7836 (mtmm) REVERT: A 327 GLU cc_start: 0.7964 (mp0) cc_final: 0.7561 (mp0) REVERT: A 356 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7244 (mtp180) REVERT: A 374 ARG cc_start: 0.8082 (mtt-85) cc_final: 0.7808 (mtt-85) REVERT: R 492 ASN cc_start: 0.8459 (m-40) cc_final: 0.7954 (m-40) REVERT: S 174 LEU cc_start: 0.8549 (tp) cc_final: 0.8285 (tp) REVERT: S 202 ARG cc_start: 0.8147 (mtm110) cc_final: 0.7860 (mtm110) REVERT: S 223 ASP cc_start: 0.7954 (m-30) cc_final: 0.7656 (m-30) REVERT: B 44 GLN cc_start: 0.7373 (mp-120) cc_final: 0.7008 (mp-120) REVERT: B 61 MET cc_start: 0.8124 (ptm) cc_final: 0.7894 (ptm) REVERT: B 68 ARG cc_start: 0.8319 (ttt-90) cc_final: 0.8093 (ttt180) REVERT: B 246 ASP cc_start: 0.7843 (m-30) cc_final: 0.7464 (m-30) REVERT: B 258 ASP cc_start: 0.8078 (t70) cc_final: 0.7837 (t70) REVERT: B 275 SER cc_start: 0.7974 (t) cc_final: 0.7753 (t) outliers start: 17 outliers final: 11 residues processed: 209 average time/residue: 0.1145 time to fit residues: 31.5204 Evaluate side-chains 210 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 198 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain R residue 386 ILE Chi-restraints excluded: chain R residue 463 THR Chi-restraints excluded: chain R residue 464 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 230 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.128839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.110394 restraints weight = 12813.105| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.89 r_work: 0.3245 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9199 Z= 0.220 Angle : 0.606 7.499 12479 Z= 0.319 Chirality : 0.044 0.157 1411 Planarity : 0.004 0.043 1581 Dihedral : 4.765 21.161 1251 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.15 % Allowed : 12.72 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.25), residues: 1134 helix: 0.87 (0.28), residues: 365 sheet: -0.30 (0.30), residues: 292 loop : -1.15 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 42 TYR 0.020 0.002 TYR A 391 PHE 0.022 0.002 PHE S 68 TRP 0.012 0.002 TRP A 234 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 9197) covalent geometry : angle 0.60512 (12475) SS BOND : bond 0.00744 ( 2) SS BOND : angle 1.78739 ( 4) hydrogen bonds : bond 0.04023 ( 401) hydrogen bonds : angle 4.82356 ( 1167) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 0.340 Fit side-chains REVERT: A 8 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7031 (mt-10) REVERT: A 207 ILE cc_start: 0.8542 (mm) cc_final: 0.8243 (mm) REVERT: A 216 LYS cc_start: 0.8485 (mppt) cc_final: 0.8193 (mppt) REVERT: A 283 ARG cc_start: 0.8260 (ttp-110) cc_final: 0.7948 (ttp80) REVERT: A 293 LYS cc_start: 0.8333 (mtmt) cc_final: 0.7892 (mtmm) REVERT: A 327 GLU cc_start: 0.7945 (mp0) cc_final: 0.7506 (mp0) REVERT: A 374 ARG cc_start: 0.8270 (mtt-85) cc_final: 0.8021 (mtt180) REVERT: R 492 ASN cc_start: 0.8506 (m-40) cc_final: 0.7988 (m-40) REVERT: S 174 LEU cc_start: 0.8675 (tp) cc_final: 0.8452 (tp) REVERT: S 202 ARG cc_start: 0.8167 (mtm110) cc_final: 0.7834 (mtm110) REVERT: S 223 ASP cc_start: 0.7909 (m-30) cc_final: 0.7541 (m-30) REVERT: B 42 ARG cc_start: 0.7366 (ttt-90) cc_final: 0.7103 (ttt-90) REVERT: B 44 GLN cc_start: 0.7458 (mp-120) cc_final: 0.6912 (mp-120) REVERT: B 223 THR cc_start: 0.7852 (t) cc_final: 0.7583 (p) REVERT: B 234 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.8404 (m-80) REVERT: B 246 ASP cc_start: 0.7881 (m-30) cc_final: 0.7485 (m-30) REVERT: B 317 CYS cc_start: 0.7600 (p) cc_final: 0.7348 (p) outliers start: 21 outliers final: 16 residues processed: 220 average time/residue: 0.1204 time to fit residues: 34.9924 Evaluate side-chains 225 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain R residue 386 ILE Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain R residue 463 THR Chi-restraints excluded: chain R residue 464 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 230 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.131011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.112440 restraints weight = 12903.038| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.97 r_work: 0.3255 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9199 Z= 0.153 Angle : 0.570 7.887 12479 Z= 0.295 Chirality : 0.042 0.168 1411 Planarity : 0.004 0.043 1581 Dihedral : 4.603 20.834 1251 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.67 % Allowed : 15.38 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.25), residues: 1134 helix: 0.98 (0.28), residues: 366 sheet: -0.19 (0.30), residues: 281 loop : -1.19 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 42 TYR 0.017 0.001 TYR A 391 PHE 0.022 0.001 PHE S 68 TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9197) covalent geometry : angle 0.56959 (12475) SS BOND : bond 0.00458 ( 2) SS BOND : angle 1.21912 ( 4) hydrogen bonds : bond 0.03628 ( 401) hydrogen bonds : angle 4.62889 ( 1167) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7340 (mt-10) cc_final: 0.7063 (mt-10) REVERT: A 216 LYS cc_start: 0.8471 (mppt) cc_final: 0.8057 (mppt) REVERT: A 293 LYS cc_start: 0.8228 (mtmt) cc_final: 0.7746 (mtmm) REVERT: A 327 GLU cc_start: 0.7975 (mp0) cc_final: 0.7488 (mp0) REVERT: A 345 PHE cc_start: 0.7849 (m-80) cc_final: 0.7390 (m-80) REVERT: A 374 ARG cc_start: 0.8296 (mtt-85) cc_final: 0.8046 (mtt180) REVERT: R 492 ASN cc_start: 0.8462 (m-40) cc_final: 0.7992 (m-40) REVERT: S 174 LEU cc_start: 0.8650 (tp) cc_final: 0.8432 (tp) REVERT: S 202 ARG cc_start: 0.8114 (mtm110) cc_final: 0.7771 (mtm110) REVERT: S 223 ASP cc_start: 0.7985 (m-30) cc_final: 0.7552 (m-30) REVERT: S 227 TYR cc_start: 0.8372 (m-80) cc_final: 0.8029 (m-80) REVERT: B 22 ARG cc_start: 0.7301 (mtt90) cc_final: 0.6818 (mtt90) REVERT: B 44 GLN cc_start: 0.7406 (mp-120) cc_final: 0.7142 (mp-120) REVERT: B 219 ARG cc_start: 0.7930 (mmt180) cc_final: 0.7465 (mpt180) REVERT: B 223 THR cc_start: 0.7861 (t) cc_final: 0.7591 (p) REVERT: B 234 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8407 (m-80) REVERT: B 246 ASP cc_start: 0.7914 (m-30) cc_final: 0.7476 (m-30) outliers start: 26 outliers final: 16 residues processed: 219 average time/residue: 0.1184 time to fit residues: 34.0869 Evaluate side-chains 218 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 347 TYR Chi-restraints excluded: chain R residue 386 ILE Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain R residue 463 THR Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 220 GLN B 230 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.130068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.111531 restraints weight = 12893.159| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.91 r_work: 0.3260 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9199 Z= 0.152 Angle : 0.562 7.275 12479 Z= 0.291 Chirality : 0.042 0.178 1411 Planarity : 0.004 0.043 1581 Dihedral : 4.535 20.486 1251 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.87 % Allowed : 16.82 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.26), residues: 1134 helix: 1.04 (0.28), residues: 362 sheet: -0.24 (0.30), residues: 281 loop : -1.13 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 42 TYR 0.016 0.001 TYR A 391 PHE 0.027 0.002 PHE S 68 TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9197) covalent geometry : angle 0.56167 (12475) SS BOND : bond 0.00692 ( 2) SS BOND : angle 1.52200 ( 4) hydrogen bonds : bond 0.03534 ( 401) hydrogen bonds : angle 4.58460 ( 1167) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 0.327 Fit side-chains REVERT: A 8 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7059 (mt-10) REVERT: A 231 ARG cc_start: 0.8139 (ptp90) cc_final: 0.7899 (ptp90) REVERT: A 293 LYS cc_start: 0.8273 (mtmt) cc_final: 0.8070 (mtpp) REVERT: A 327 GLU cc_start: 0.7950 (mp0) cc_final: 0.7472 (mp0) REVERT: A 345 PHE cc_start: 0.7926 (m-80) cc_final: 0.7469 (m-80) REVERT: A 374 ARG cc_start: 0.8338 (mtt-85) cc_final: 0.8035 (mtt180) REVERT: A 392 GLU cc_start: 0.6700 (pt0) cc_final: 0.6451 (pt0) REVERT: R 290 SER cc_start: 0.7688 (t) cc_final: 0.7469 (p) REVERT: R 492 ASN cc_start: 0.8478 (m-40) cc_final: 0.8000 (m-40) REVERT: S 174 LEU cc_start: 0.8680 (tp) cc_final: 0.8465 (tp) REVERT: S 202 ARG cc_start: 0.8139 (mtm110) cc_final: 0.7821 (mtm110) REVERT: S 223 ASP cc_start: 0.7971 (m-30) cc_final: 0.7538 (m-30) REVERT: S 227 TYR cc_start: 0.8430 (m-80) cc_final: 0.8105 (m-80) REVERT: B 22 ARG cc_start: 0.7412 (mtt90) cc_final: 0.6892 (mtt90) REVERT: B 42 ARG cc_start: 0.7300 (ttt-90) cc_final: 0.7016 (ttt-90) REVERT: B 44 GLN cc_start: 0.7504 (mp-120) cc_final: 0.6688 (mp-120) REVERT: B 55 LEU cc_start: 0.8266 (mp) cc_final: 0.7992 (mp) REVERT: B 59 TYR cc_start: 0.7766 (OUTLIER) cc_final: 0.7485 (m-10) REVERT: B 219 ARG cc_start: 0.7845 (mmt180) cc_final: 0.7494 (mpt180) REVERT: B 223 THR cc_start: 0.7860 (t) cc_final: 0.7593 (p) REVERT: B 234 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8437 (m-80) outliers start: 28 outliers final: 21 residues processed: 223 average time/residue: 0.1224 time to fit residues: 36.1209 Evaluate side-chains 229 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 347 TYR Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 386 ILE Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain R residue 423 THR Chi-restraints excluded: chain R residue 463 THR Chi-restraints excluded: chain R residue 508 CYS Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 98 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 39 optimal weight: 0.0070 chunk 49 optimal weight: 1.9990 chunk 104 optimal weight: 0.2980 chunk 34 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 0.0370 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.133637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.115128 restraints weight = 12867.607| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.99 r_work: 0.3303 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9199 Z= 0.102 Angle : 0.535 8.032 12479 Z= 0.276 Chirality : 0.041 0.186 1411 Planarity : 0.004 0.040 1581 Dihedral : 4.318 20.126 1251 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.18 % Allowed : 17.74 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.26), residues: 1134 helix: 1.32 (0.29), residues: 358 sheet: -0.28 (0.31), residues: 273 loop : -1.10 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 385 TYR 0.011 0.001 TYR R 381 PHE 0.022 0.001 PHE S 68 TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 9197) covalent geometry : angle 0.53405 (12475) SS BOND : bond 0.00591 ( 2) SS BOND : angle 1.65313 ( 4) hydrogen bonds : bond 0.03210 ( 401) hydrogen bonds : angle 4.40537 ( 1167) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7308 (mt-10) cc_final: 0.7009 (mt-10) REVERT: A 216 LYS cc_start: 0.8474 (mppt) cc_final: 0.8017 (mppt) REVERT: A 246 PHE cc_start: 0.8192 (t80) cc_final: 0.7955 (t80) REVERT: A 327 GLU cc_start: 0.7936 (mp0) cc_final: 0.7444 (mp0) REVERT: A 345 PHE cc_start: 0.7858 (m-80) cc_final: 0.7445 (m-80) REVERT: R 492 ASN cc_start: 0.8370 (m-40) cc_final: 0.7986 (m-40) REVERT: S 32 PHE cc_start: 0.8199 (m-80) cc_final: 0.7549 (m-80) REVERT: S 174 LEU cc_start: 0.8491 (tp) cc_final: 0.8290 (tp) REVERT: S 202 ARG cc_start: 0.8069 (mtm110) cc_final: 0.7797 (mtm110) REVERT: S 223 ASP cc_start: 0.7944 (m-30) cc_final: 0.7604 (m-30) REVERT: B 22 ARG cc_start: 0.7246 (mtt90) cc_final: 0.6810 (mtt90) REVERT: B 44 GLN cc_start: 0.7435 (mp-120) cc_final: 0.7198 (mp-120) REVERT: B 55 LEU cc_start: 0.8275 (mp) cc_final: 0.7979 (mp) REVERT: B 59 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.7232 (m-10) REVERT: B 124 TYR cc_start: 0.8125 (m-80) cc_final: 0.7874 (m-80) REVERT: B 156 GLN cc_start: 0.8250 (mt0) cc_final: 0.8033 (mt0) REVERT: B 210 LEU cc_start: 0.8435 (tp) cc_final: 0.8029 (tp) REVERT: B 219 ARG cc_start: 0.7839 (mmt180) cc_final: 0.7421 (mpt180) REVERT: B 223 THR cc_start: 0.7788 (t) cc_final: 0.7530 (p) REVERT: B 234 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8450 (m-80) REVERT: B 258 ASP cc_start: 0.8053 (t70) cc_final: 0.7719 (t70) REVERT: B 275 SER cc_start: 0.7997 (t) cc_final: 0.7740 (p) REVERT: B 283 ARG cc_start: 0.8455 (tpt170) cc_final: 0.8227 (tpt170) outliers start: 31 outliers final: 22 residues processed: 230 average time/residue: 0.1255 time to fit residues: 37.7147 Evaluate side-chains 230 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 347 TYR Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 386 ILE Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain R residue 463 THR Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain R residue 508 CYS Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 78 optimal weight: 0.0060 chunk 53 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 31 optimal weight: 0.0010 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.132784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114197 restraints weight = 12912.142| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.99 r_work: 0.3291 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9199 Z= 0.112 Angle : 0.539 7.338 12479 Z= 0.278 Chirality : 0.041 0.194 1411 Planarity : 0.003 0.039 1581 Dihedral : 4.267 20.092 1251 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.28 % Allowed : 18.05 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.26), residues: 1134 helix: 1.32 (0.29), residues: 363 sheet: -0.23 (0.31), residues: 266 loop : -1.08 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 385 TYR 0.012 0.001 TYR A 391 PHE 0.032 0.001 PHE S 68 TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9197) covalent geometry : angle 0.53871 (12475) SS BOND : bond 0.00676 ( 2) SS BOND : angle 0.96376 ( 4) hydrogen bonds : bond 0.03204 ( 401) hydrogen bonds : angle 4.37891 ( 1167) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 209 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7021 (mt-10) REVERT: A 216 LYS cc_start: 0.8462 (mppt) cc_final: 0.8024 (mppt) REVERT: A 231 ARG cc_start: 0.8063 (ptp90) cc_final: 0.7823 (ptp90) REVERT: A 246 PHE cc_start: 0.8211 (t80) cc_final: 0.7968 (t80) REVERT: A 293 LYS cc_start: 0.8267 (mtpp) cc_final: 0.7693 (mtmm) REVERT: A 327 GLU cc_start: 0.7906 (mp0) cc_final: 0.7417 (mp0) REVERT: A 345 PHE cc_start: 0.7884 (m-80) cc_final: 0.7469 (m-80) REVERT: A 374 ARG cc_start: 0.8344 (mtt-85) cc_final: 0.8132 (mtt180) REVERT: R 492 ASN cc_start: 0.8413 (m-40) cc_final: 0.8016 (m-40) REVERT: S 32 PHE cc_start: 0.8231 (m-80) cc_final: 0.8009 (m-80) REVERT: S 202 ARG cc_start: 0.8083 (mtm110) cc_final: 0.7803 (mtm110) REVERT: S 223 ASP cc_start: 0.7946 (m-30) cc_final: 0.7589 (m-30) REVERT: B 22 ARG cc_start: 0.7280 (mtt90) cc_final: 0.6784 (mtt90) REVERT: B 44 GLN cc_start: 0.7452 (mp-120) cc_final: 0.7225 (mp-120) REVERT: B 55 LEU cc_start: 0.8260 (mp) cc_final: 0.8007 (mp) REVERT: B 59 TYR cc_start: 0.7694 (OUTLIER) cc_final: 0.7346 (m-10) REVERT: B 124 TYR cc_start: 0.8128 (m-80) cc_final: 0.7895 (m-80) REVERT: B 210 LEU cc_start: 0.8481 (tp) cc_final: 0.8053 (tp) REVERT: B 219 ARG cc_start: 0.7908 (mmt180) cc_final: 0.7466 (mpt180) REVERT: B 223 THR cc_start: 0.7778 (t) cc_final: 0.7515 (p) REVERT: B 234 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8466 (m-80) REVERT: B 275 SER cc_start: 0.8031 (t) cc_final: 0.7747 (p) REVERT: B 283 ARG cc_start: 0.8450 (tpt170) cc_final: 0.8062 (tpt170) outliers start: 32 outliers final: 24 residues processed: 227 average time/residue: 0.1193 time to fit residues: 35.7801 Evaluate side-chains 232 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 347 TYR Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 386 ILE Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain R residue 423 THR Chi-restraints excluded: chain R residue 463 THR Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain R residue 508 CYS Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 0.4980 chunk 94 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 41 optimal weight: 7.9990 chunk 37 optimal weight: 0.3980 chunk 104 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.132881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.114245 restraints weight = 12877.334| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.92 r_work: 0.3291 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9199 Z= 0.124 Angle : 0.550 7.415 12479 Z= 0.283 Chirality : 0.042 0.201 1411 Planarity : 0.004 0.039 1581 Dihedral : 4.298 19.989 1251 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.97 % Allowed : 18.77 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.26), residues: 1134 helix: 1.44 (0.29), residues: 357 sheet: -0.23 (0.31), residues: 266 loop : -1.09 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 68 TYR 0.013 0.001 TYR A 391 PHE 0.014 0.001 PHE S 68 TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9197) covalent geometry : angle 0.55004 (12475) SS BOND : bond 0.00679 ( 2) SS BOND : angle 1.30819 ( 4) hydrogen bonds : bond 0.03254 ( 401) hydrogen bonds : angle 4.38624 ( 1167) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7324 (mt-10) cc_final: 0.7037 (mt-10) REVERT: A 216 LYS cc_start: 0.8420 (mppt) cc_final: 0.8033 (mppt) REVERT: A 231 ARG cc_start: 0.8051 (ptp90) cc_final: 0.7848 (ptp90) REVERT: A 246 PHE cc_start: 0.8218 (t80) cc_final: 0.7983 (t80) REVERT: A 292 ASN cc_start: 0.8365 (t0) cc_final: 0.8151 (t0) REVERT: A 293 LYS cc_start: 0.8376 (mtpp) cc_final: 0.7651 (mtmm) REVERT: A 327 GLU cc_start: 0.7878 (mp0) cc_final: 0.7403 (mp0) REVERT: A 345 PHE cc_start: 0.7945 (m-80) cc_final: 0.7520 (m-80) REVERT: R 492 ASN cc_start: 0.8453 (m-40) cc_final: 0.8038 (m-40) REVERT: S 32 PHE cc_start: 0.8242 (m-80) cc_final: 0.7945 (m-80) REVERT: S 68 PHE cc_start: 0.7392 (m-10) cc_final: 0.7021 (m-10) REVERT: S 202 ARG cc_start: 0.8123 (mtm110) cc_final: 0.7859 (mtm110) REVERT: S 223 ASP cc_start: 0.7917 (m-30) cc_final: 0.7540 (m-30) REVERT: B 22 ARG cc_start: 0.7402 (mtt90) cc_final: 0.6841 (mtt90) REVERT: B 44 GLN cc_start: 0.7509 (mp-120) cc_final: 0.7284 (mp-120) REVERT: B 55 LEU cc_start: 0.8257 (mp) cc_final: 0.8007 (mp) REVERT: B 59 TYR cc_start: 0.7721 (OUTLIER) cc_final: 0.7448 (m-10) REVERT: B 210 LEU cc_start: 0.8522 (tp) cc_final: 0.8095 (tp) REVERT: B 219 ARG cc_start: 0.7954 (mmt180) cc_final: 0.7623 (mpt180) REVERT: B 223 THR cc_start: 0.7769 (t) cc_final: 0.7497 (p) REVERT: B 234 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.8455 (m-80) REVERT: B 283 ARG cc_start: 0.8477 (tpt170) cc_final: 0.8106 (tpt170) outliers start: 29 outliers final: 23 residues processed: 224 average time/residue: 0.1102 time to fit residues: 32.6682 Evaluate side-chains 230 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 304 PHE Chi-restraints excluded: chain R residue 347 TYR Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 386 ILE Chi-restraints excluded: chain R residue 423 THR Chi-restraints excluded: chain R residue 463 THR Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain R residue 508 CYS Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 66 optimal weight: 0.0010 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.132455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.113760 restraints weight = 12941.711| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.93 r_work: 0.3283 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9199 Z= 0.137 Angle : 0.564 8.355 12479 Z= 0.289 Chirality : 0.042 0.207 1411 Planarity : 0.004 0.039 1581 Dihedral : 4.332 19.821 1251 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.77 % Allowed : 19.49 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.26), residues: 1134 helix: 1.42 (0.29), residues: 357 sheet: -0.29 (0.30), residues: 283 loop : -1.04 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 385 TYR 0.014 0.001 TYR A 391 PHE 0.030 0.001 PHE S 239 TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9197) covalent geometry : angle 0.56341 (12475) SS BOND : bond 0.00734 ( 2) SS BOND : angle 1.24544 ( 4) hydrogen bonds : bond 0.03318 ( 401) hydrogen bonds : angle 4.46204 ( 1167) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7051 (mt-10) REVERT: A 216 LYS cc_start: 0.8426 (mppt) cc_final: 0.8045 (mppt) REVERT: A 231 ARG cc_start: 0.8004 (ptp90) cc_final: 0.7786 (ptp90) REVERT: A 246 PHE cc_start: 0.8226 (t80) cc_final: 0.8002 (t80) REVERT: A 292 ASN cc_start: 0.8412 (t0) cc_final: 0.8170 (t0) REVERT: A 327 GLU cc_start: 0.7901 (mp0) cc_final: 0.7416 (mp0) REVERT: A 345 PHE cc_start: 0.7945 (m-80) cc_final: 0.7519 (m-80) REVERT: A 374 ARG cc_start: 0.8365 (mtt-85) cc_final: 0.8127 (mtt180) REVERT: R 492 ASN cc_start: 0.8473 (m-40) cc_final: 0.8059 (m-40) REVERT: S 32 PHE cc_start: 0.8280 (m-80) cc_final: 0.7973 (m-80) REVERT: S 202 ARG cc_start: 0.8120 (mtm110) cc_final: 0.7808 (mtm110) REVERT: S 223 ASP cc_start: 0.7910 (m-30) cc_final: 0.7518 (m-30) REVERT: S 224 VAL cc_start: 0.8245 (p) cc_final: 0.8042 (t) REVERT: B 44 GLN cc_start: 0.7518 (mp-120) cc_final: 0.7310 (mp-120) REVERT: B 47 THR cc_start: 0.8392 (m) cc_final: 0.8103 (p) REVERT: B 55 LEU cc_start: 0.8266 (mp) cc_final: 0.7996 (mp) REVERT: B 59 TYR cc_start: 0.7773 (OUTLIER) cc_final: 0.7478 (m-10) REVERT: B 68 ARG cc_start: 0.8030 (ttt180) cc_final: 0.7803 (ttt-90) REVERT: B 210 LEU cc_start: 0.8515 (tp) cc_final: 0.8071 (tp) REVERT: B 219 ARG cc_start: 0.7924 (mmt180) cc_final: 0.7581 (mpt180) REVERT: B 220 GLN cc_start: 0.8198 (mt0) cc_final: 0.7736 (mt0) REVERT: B 223 THR cc_start: 0.7775 (t) cc_final: 0.7518 (p) REVERT: B 234 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.8458 (m-80) REVERT: B 258 ASP cc_start: 0.8033 (t70) cc_final: 0.7582 (t70) REVERT: B 275 SER cc_start: 0.7999 (t) cc_final: 0.7742 (p) outliers start: 27 outliers final: 21 residues processed: 221 average time/residue: 0.1207 time to fit residues: 35.4965 Evaluate side-chains 230 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 304 PHE Chi-restraints excluded: chain R residue 347 TYR Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 386 ILE Chi-restraints excluded: chain R residue 423 THR Chi-restraints excluded: chain R residue 463 THR Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain R residue 508 CYS Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 35 optimal weight: 0.0570 chunk 97 optimal weight: 0.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.132519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.113802 restraints weight = 12754.251| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.91 r_work: 0.3278 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9199 Z= 0.148 Angle : 0.577 8.962 12479 Z= 0.296 Chirality : 0.043 0.185 1411 Planarity : 0.004 0.040 1581 Dihedral : 4.405 20.126 1251 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.56 % Allowed : 19.90 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.26), residues: 1134 helix: 1.39 (0.29), residues: 353 sheet: -0.31 (0.30), residues: 283 loop : -0.99 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 52 TYR 0.015 0.001 TYR A 391 PHE 0.027 0.001 PHE S 239 TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9197) covalent geometry : angle 0.57642 (12475) SS BOND : bond 0.00741 ( 2) SS BOND : angle 1.25006 ( 4) hydrogen bonds : bond 0.03383 ( 401) hydrogen bonds : angle 4.51801 ( 1167) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7343 (mt-10) cc_final: 0.7054 (mt-10) REVERT: A 216 LYS cc_start: 0.8456 (mppt) cc_final: 0.8152 (mppt) REVERT: A 231 ARG cc_start: 0.7975 (ptp90) cc_final: 0.7764 (ptp90) REVERT: A 246 PHE cc_start: 0.8238 (t80) cc_final: 0.7999 (t80) REVERT: A 292 ASN cc_start: 0.8383 (t0) cc_final: 0.8154 (t0) REVERT: A 293 LYS cc_start: 0.8390 (mtpp) cc_final: 0.7641 (mtmm) REVERT: A 327 GLU cc_start: 0.7883 (mp0) cc_final: 0.7398 (mp0) REVERT: A 345 PHE cc_start: 0.7948 (m-80) cc_final: 0.7513 (m-80) REVERT: A 374 ARG cc_start: 0.8365 (mtt-85) cc_final: 0.8116 (mtt180) REVERT: R 492 ASN cc_start: 0.8473 (m-40) cc_final: 0.8038 (m-40) REVERT: S 32 PHE cc_start: 0.8283 (m-80) cc_final: 0.7671 (m-80) REVERT: S 83 MET cc_start: 0.6324 (ttp) cc_final: 0.6031 (ttm) REVERT: S 202 ARG cc_start: 0.8143 (mtm110) cc_final: 0.7809 (mtm110) REVERT: S 223 ASP cc_start: 0.7912 (m-30) cc_final: 0.7529 (m-30) REVERT: S 230 MET cc_start: 0.7825 (mmm) cc_final: 0.7577 (tpp) REVERT: B 47 THR cc_start: 0.8391 (m) cc_final: 0.8109 (p) REVERT: B 55 LEU cc_start: 0.8254 (mp) cc_final: 0.7988 (mp) REVERT: B 59 TYR cc_start: 0.7809 (OUTLIER) cc_final: 0.7563 (m-10) REVERT: B 68 ARG cc_start: 0.8061 (ttt180) cc_final: 0.7743 (ttt90) REVERT: B 210 LEU cc_start: 0.8517 (tp) cc_final: 0.8074 (tp) REVERT: B 219 ARG cc_start: 0.7941 (mmt180) cc_final: 0.7642 (mpt180) REVERT: B 220 GLN cc_start: 0.8200 (mt0) cc_final: 0.7823 (mt0) REVERT: B 223 THR cc_start: 0.7796 (t) cc_final: 0.7548 (p) REVERT: B 234 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8458 (m-80) REVERT: B 258 ASP cc_start: 0.7948 (t70) cc_final: 0.7611 (t70) REVERT: B 275 SER cc_start: 0.7999 (t) cc_final: 0.7720 (p) outliers start: 25 outliers final: 22 residues processed: 221 average time/residue: 0.1200 time to fit residues: 35.2379 Evaluate side-chains 231 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 347 TYR Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 386 ILE Chi-restraints excluded: chain R residue 423 THR Chi-restraints excluded: chain R residue 463 THR Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain R residue 508 CYS Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 85 optimal weight: 0.0470 chunk 92 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN S 142 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.133414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.114662 restraints weight = 12615.523| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.91 r_work: 0.3288 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9199 Z= 0.131 Angle : 0.567 8.687 12479 Z= 0.291 Chirality : 0.042 0.195 1411 Planarity : 0.004 0.040 1581 Dihedral : 4.361 20.410 1251 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.77 % Allowed : 20.10 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.26), residues: 1134 helix: 1.42 (0.29), residues: 353 sheet: -0.30 (0.30), residues: 283 loop : -0.99 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 52 TYR 0.013 0.001 TYR A 391 PHE 0.024 0.001 PHE S 239 TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9197) covalent geometry : angle 0.56707 (12475) SS BOND : bond 0.00691 ( 2) SS BOND : angle 1.21971 ( 4) hydrogen bonds : bond 0.03333 ( 401) hydrogen bonds : angle 4.48490 ( 1167) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2517.08 seconds wall clock time: 43 minutes 53.78 seconds (2633.78 seconds total)