Starting phenix.real_space_refine on Thu Feb 13 10:39:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eq1_31254/02_2025/7eq1_31254.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eq1_31254/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7eq1_31254/02_2025/7eq1_31254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eq1_31254/02_2025/7eq1_31254.map" model { file = "/net/cci-nas-00/data/ceres_data/7eq1_31254/02_2025/7eq1_31254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eq1_31254/02_2025/7eq1_31254.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.16, per 1000 atoms: 0.57 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: 2.23 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.12 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: 2.63 Time building geometry restraints manager: 2.58 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.650 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.320 ------------------------------------------------------------------------------- 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 9197 Z= 0.210 Angle : 0.584 8.383 12475 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (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 TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS B 311 PHE 0.028 0.002 PHE S 239 TYR 0.030 0.002 TYR B 59 ARG 0.006 0.000 ARG A 283 *********************** 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 : 1.015 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: 0.2624 time to fit residues: 67.4800 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 : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 88 ASN B 220 GLN ** 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 = 0.3666 r_free = 0.3666 target = 0.132053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.113529 restraints weight = 12727.218| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.95 r_work: 0.3277 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9197 Z= 0.213 Angle : 0.578 7.085 12475 Z= 0.303 Chirality : 0.043 0.175 1411 Planarity : 0.004 0.041 1581 Dihedral : 4.586 20.888 1251 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.64 % Allowed : 8.92 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.26), residues: 1134 helix: 0.76 (0.29), residues: 374 sheet: -0.20 (0.30), residues: 284 loop : -1.24 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 PHE 0.026 0.002 PHE S 68 TYR 0.015 0.001 TYR A 391 ARG 0.008 0.001 ARG B 42 *********************** 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 219 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6950 (mt-10) REVERT: A 207 ILE cc_start: 0.8515 (mm) cc_final: 0.8192 (mm) REVERT: A 216 LYS cc_start: 0.8488 (mppt) cc_final: 0.8040 (mppt) REVERT: A 293 LYS cc_start: 0.8222 (mtmt) cc_final: 0.7779 (mtmm) REVERT: A 327 GLU cc_start: 0.7964 (mp0) cc_final: 0.7562 (mp0) REVERT: A 356 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7240 (mtp180) REVERT: A 374 ARG cc_start: 0.8078 (mtt-85) cc_final: 0.7813 (mtt-85) REVERT: R 492 ASN cc_start: 0.8456 (m-40) cc_final: 0.7963 (m-40) REVERT: S 20 LEU cc_start: 0.7998 (mp) cc_final: 0.7783 (mp) REVERT: S 174 LEU cc_start: 0.8545 (tp) cc_final: 0.8282 (tp) REVERT: S 202 ARG cc_start: 0.8145 (mtm110) cc_final: 0.7859 (mtm110) REVERT: S 223 ASP cc_start: 0.7976 (m-30) cc_final: 0.7677 (m-30) REVERT: B 42 ARG cc_start: 0.7253 (ttt-90) cc_final: 0.7016 (ttt-90) REVERT: B 44 GLN cc_start: 0.7397 (mp-120) cc_final: 0.7033 (mp-120) REVERT: B 61 MET cc_start: 0.8122 (ptm) cc_final: 0.7889 (ptm) REVERT: B 68 ARG cc_start: 0.8313 (ttt-90) cc_final: 0.8089 (ttt180) REVERT: B 246 ASP cc_start: 0.7834 (m-30) cc_final: 0.7457 (m-30) REVERT: B 258 ASP cc_start: 0.8087 (t70) cc_final: 0.7856 (t70) REVERT: B 275 SER cc_start: 0.7972 (t) cc_final: 0.7758 (t) REVERT: B 315 VAL cc_start: 0.7253 (t) cc_final: 0.6952 (t) outliers start: 16 outliers final: 11 residues processed: 208 average time/residue: 0.2697 time to fit residues: 74.7661 Evaluate side-chains 209 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 197 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 65 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.130539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.111964 restraints weight = 12868.641| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.91 r_work: 0.3265 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9197 Z= 0.229 Angle : 0.564 7.035 12475 Z= 0.295 Chirality : 0.043 0.157 1411 Planarity : 0.004 0.041 1581 Dihedral : 4.543 20.324 1251 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.74 % Allowed : 13.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.26), residues: 1134 helix: 0.99 (0.28), residues: 366 sheet: -0.11 (0.30), residues: 281 loop : -1.15 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS B 225 PHE 0.019 0.001 PHE S 68 TYR 0.017 0.001 TYR A 391 ARG 0.004 0.000 ARG B 96 *********************** 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 215 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7308 (mt-10) cc_final: 0.7030 (mt-10) REVERT: A 216 LYS cc_start: 0.8494 (mppt) cc_final: 0.8092 (mppt) REVERT: A 283 ARG cc_start: 0.8240 (ttp-110) cc_final: 0.7890 (ttp80) REVERT: A 293 LYS cc_start: 0.8295 (mtmt) cc_final: 0.7839 (mtmm) REVERT: A 327 GLU cc_start: 0.7926 (mp0) cc_final: 0.7517 (mp0) REVERT: A 374 ARG cc_start: 0.8260 (mtt-85) cc_final: 0.7944 (mtt-85) REVERT: R 492 ASN cc_start: 0.8497 (m-40) cc_final: 0.8020 (m-40) REVERT: S 174 LEU cc_start: 0.8589 (tp) cc_final: 0.8369 (tp) REVERT: S 202 ARG cc_start: 0.8161 (mtm110) cc_final: 0.7877 (mtm110) REVERT: S 223 ASP cc_start: 0.7920 (m-30) cc_final: 0.7599 (m-30) REVERT: B 61 MET cc_start: 0.8091 (ptm) cc_final: 0.7876 (ptm) REVERT: B 68 ARG cc_start: 0.8260 (ttt-90) cc_final: 0.8010 (ttt180) REVERT: B 223 THR cc_start: 0.7757 (t) cc_final: 0.7495 (p) REVERT: B 234 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8431 (m-80) REVERT: B 275 SER cc_start: 0.7897 (t) cc_final: 0.7680 (t) REVERT: B 317 CYS cc_start: 0.7562 (p) cc_final: 0.7300 (p) outliers start: 17 outliers final: 14 residues processed: 205 average time/residue: 0.2582 time to fit residues: 70.2417 Evaluate side-chains 210 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 195 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 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 54 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 31 optimal weight: 0.0370 chunk 55 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 68 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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 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 = 0.3666 r_free = 0.3666 target = 0.131984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113388 restraints weight = 12833.684| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.97 r_work: 0.3280 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9197 Z= 0.166 Angle : 0.540 7.752 12475 Z= 0.279 Chirality : 0.042 0.172 1411 Planarity : 0.004 0.043 1581 Dihedral : 4.377 19.805 1251 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.26 % Allowed : 14.87 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.26), residues: 1134 helix: 1.33 (0.29), residues: 352 sheet: -0.15 (0.30), residues: 284 loop : -1.24 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 PHE 0.020 0.001 PHE S 239 TYR 0.013 0.001 TYR A 391 ARG 0.003 0.000 ARG B 96 *********************** 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 224 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 1.021 Fit side-chains REVERT: A 8 GLU cc_start: 0.7297 (mt-10) cc_final: 0.7021 (mt-10) REVERT: A 246 PHE cc_start: 0.8237 (t80) cc_final: 0.8034 (t80) REVERT: A 283 ARG cc_start: 0.8185 (ttp-110) cc_final: 0.7976 (ttp80) REVERT: A 327 GLU cc_start: 0.7942 (mp0) cc_final: 0.7513 (mp0) REVERT: A 345 PHE cc_start: 0.7835 (m-80) cc_final: 0.7363 (m-80) REVERT: R 492 ASN cc_start: 0.8425 (m-40) cc_final: 0.8006 (m-40) REVERT: S 174 LEU cc_start: 0.8516 (tp) cc_final: 0.8274 (tp) REVERT: S 202 ARG cc_start: 0.8100 (mtm110) cc_final: 0.7802 (mtm110) REVERT: S 223 ASP cc_start: 0.8019 (m-30) cc_final: 0.7681 (m-30) REVERT: B 22 ARG cc_start: 0.7201 (mtt90) cc_final: 0.6921 (mtt90) REVERT: B 42 ARG cc_start: 0.7444 (ttt-90) cc_final: 0.7009 (ttt-90) REVERT: B 44 GLN cc_start: 0.7502 (mp-120) cc_final: 0.6745 (mp10) REVERT: B 61 MET cc_start: 0.8182 (ptm) cc_final: 0.7926 (ptm) REVERT: B 68 ARG cc_start: 0.8265 (ttt-90) cc_final: 0.8033 (ttt180) REVERT: B 210 LEU cc_start: 0.8428 (tp) cc_final: 0.8013 (tp) REVERT: B 219 ARG cc_start: 0.7901 (mmt180) cc_final: 0.7459 (mpt180) REVERT: B 223 THR cc_start: 0.7740 (t) cc_final: 0.7468 (p) REVERT: B 234 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8435 (m-80) REVERT: B 258 ASP cc_start: 0.8143 (t70) cc_final: 0.7871 (t70) REVERT: B 283 ARG cc_start: 0.8425 (tpt170) cc_final: 0.8016 (tpt170) REVERT: B 317 CYS cc_start: 0.7600 (p) cc_final: 0.7345 (p) outliers start: 22 outliers final: 11 residues processed: 215 average time/residue: 0.2692 time to fit residues: 76.2260 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 : 0.956 ------------------------------------------------------------------------------- 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 R residue 239 LEU 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: 1.9990 chunk 17 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 59 optimal weight: 0.0070 chunk 67 optimal weight: 0.7980 chunk 109 optimal weight: 8.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN 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 = 0.3640 r_free = 0.3640 target = 0.131491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.112901 restraints weight = 12810.751| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.92 r_work: 0.3263 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9197 Z= 0.219 Angle : 0.552 6.727 12475 Z= 0.287 Chirality : 0.042 0.178 1411 Planarity : 0.004 0.042 1581 Dihedral : 4.444 19.762 1251 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.46 % Allowed : 16.62 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.26), residues: 1134 helix: 1.28 (0.28), residues: 357 sheet: -0.16 (0.30), residues: 281 loop : -1.14 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS A 362 PHE 0.022 0.001 PHE S 68 TYR 0.016 0.001 TYR A 391 ARG 0.003 0.000 ARG B 251 *********************** 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 233 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 209 time to evaluate : 0.946 Fit side-chains REVERT: A 8 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7023 (mt-10) REVERT: A 216 LYS cc_start: 0.8447 (mppt) cc_final: 0.8080 (mppt) REVERT: A 292 ASN cc_start: 0.8353 (t0) cc_final: 0.8076 (t0) REVERT: A 293 LYS cc_start: 0.8345 (mtpp) cc_final: 0.7601 (mtmm) REVERT: A 327 GLU cc_start: 0.7935 (mp0) cc_final: 0.7496 (mp0) REVERT: A 345 PHE cc_start: 0.7904 (m-80) cc_final: 0.7413 (m-80) REVERT: A 374 ARG cc_start: 0.8309 (mtt-85) cc_final: 0.8024 (mtt180) REVERT: R 492 ASN cc_start: 0.8494 (m-40) cc_final: 0.8039 (m-40) REVERT: S 174 LEU cc_start: 0.8596 (tp) cc_final: 0.8364 (tp) REVERT: S 202 ARG cc_start: 0.8162 (mtm110) cc_final: 0.7870 (mtm110) REVERT: S 223 ASP cc_start: 0.7963 (m-30) cc_final: 0.7593 (m-30) REVERT: B 42 ARG cc_start: 0.7503 (ttt-90) cc_final: 0.7039 (ttt-90) REVERT: B 44 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.6741 (mp10) REVERT: B 59 TYR cc_start: 0.7704 (OUTLIER) cc_final: 0.7426 (m-10) REVERT: B 61 MET cc_start: 0.8190 (ptm) cc_final: 0.7883 (ptm) REVERT: B 210 LEU cc_start: 0.8457 (tp) cc_final: 0.8048 (tp) REVERT: B 219 ARG cc_start: 0.7854 (mmt180) cc_final: 0.7431 (mpt180) REVERT: B 223 THR cc_start: 0.7801 (t) cc_final: 0.7545 (p) REVERT: B 234 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.8426 (m-80) REVERT: B 317 CYS cc_start: 0.7620 (p) cc_final: 0.7338 (p) outliers start: 24 outliers final: 16 residues processed: 219 average time/residue: 0.2621 time to fit residues: 75.8970 Evaluate side-chains 220 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 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 A residue 386 MET 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 B residue 44 GLN 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 59 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 78 optimal weight: 0.0170 chunk 99 optimal weight: 3.9990 overall best weight: 0.9424 ------------------------------------------------------------------------------- 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.131029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.112521 restraints weight = 12709.330| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.89 r_work: 0.3258 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9197 Z= 0.243 Angle : 0.567 6.933 12475 Z= 0.294 Chirality : 0.043 0.178 1411 Planarity : 0.004 0.044 1581 Dihedral : 4.520 20.277 1251 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.08 % Allowed : 16.72 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.26), residues: 1134 helix: 1.27 (0.28), residues: 357 sheet: -0.20 (0.30), residues: 282 loop : -1.13 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS B 225 PHE 0.027 0.002 PHE S 68 TYR 0.017 0.001 TYR A 391 ARG 0.003 0.000 ARG B 68 *********************** 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 238 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 0.972 Fit side-chains REVERT: A 8 GLU cc_start: 0.7349 (mt-10) cc_final: 0.7069 (mt-10) REVERT: A 216 LYS cc_start: 0.8444 (mppt) cc_final: 0.8165 (mppt) REVERT: A 292 ASN cc_start: 0.8365 (t0) cc_final: 0.8016 (t0) REVERT: A 327 GLU cc_start: 0.7920 (mp0) cc_final: 0.7456 (mp0) REVERT: A 374 ARG cc_start: 0.8247 (mtt-85) cc_final: 0.7927 (mtt-85) REVERT: R 492 ASN cc_start: 0.8486 (m-40) cc_final: 0.8023 (m-40) REVERT: S 32 PHE cc_start: 0.8235 (m-80) cc_final: 0.7940 (m-80) REVERT: S 174 LEU cc_start: 0.8610 (tp) cc_final: 0.8378 (tp) REVERT: S 202 ARG cc_start: 0.8152 (mtm110) cc_final: 0.7823 (mtm110) REVERT: S 223 ASP cc_start: 0.7924 (m-30) cc_final: 0.7497 (m-30) REVERT: S 227 TYR cc_start: 0.8380 (m-80) cc_final: 0.8030 (m-80) REVERT: B 22 ARG cc_start: 0.7297 (mtt90) cc_final: 0.7039 (mtt90) REVERT: B 42 ARG cc_start: 0.7418 (ttt-90) cc_final: 0.6984 (ttt-90) REVERT: B 44 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.6756 (mp10) REVERT: B 59 TYR cc_start: 0.7756 (OUTLIER) cc_final: 0.7549 (m-10) REVERT: B 61 MET cc_start: 0.8176 (ptm) cc_final: 0.7937 (ptm) REVERT: B 68 ARG cc_start: 0.8293 (ttt-90) cc_final: 0.8051 (ttt180) REVERT: B 219 ARG cc_start: 0.7850 (mmt180) cc_final: 0.7552 (mmp80) REVERT: B 223 THR cc_start: 0.7786 (t) cc_final: 0.7541 (p) REVERT: B 234 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.8435 (m-80) REVERT: B 258 ASP cc_start: 0.8139 (t70) cc_final: 0.7822 (t70) REVERT: B 275 SER cc_start: 0.7924 (t) cc_final: 0.7694 (t) outliers start: 30 outliers final: 22 residues processed: 220 average time/residue: 0.2602 time to fit residues: 75.8703 Evaluate side-chains 231 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 A residue 386 MET 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 B residue 44 GLN 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 60 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.131130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.112448 restraints weight = 12872.761| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.93 r_work: 0.3264 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9197 Z= 0.213 Angle : 0.563 7.097 12475 Z= 0.290 Chirality : 0.042 0.187 1411 Planarity : 0.004 0.043 1581 Dihedral : 4.484 20.262 1251 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.28 % Allowed : 17.85 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.26), residues: 1134 helix: 1.29 (0.29), residues: 353 sheet: -0.29 (0.31), residues: 261 loop : -1.02 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 PHE 0.017 0.001 PHE S 68 TYR 0.016 0.001 TYR A 391 ARG 0.005 0.000 ARG A 283 *********************** 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 240 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 208 time to evaluate : 0.989 Fit side-chains REVERT: A 8 GLU cc_start: 0.7302 (mt-10) cc_final: 0.7021 (mt-10) REVERT: A 216 LYS cc_start: 0.8443 (mppt) cc_final: 0.8153 (mppt) REVERT: A 231 ARG cc_start: 0.8158 (ptp90) cc_final: 0.7923 (ptp90) REVERT: A 292 ASN cc_start: 0.8378 (t0) cc_final: 0.8000 (t0) REVERT: A 327 GLU cc_start: 0.7910 (mp0) cc_final: 0.7441 (mp0) REVERT: A 370 GLU cc_start: 0.7312 (pp20) cc_final: 0.6976 (pp20) REVERT: A 374 ARG cc_start: 0.8285 (mtt-85) cc_final: 0.8017 (mtt180) REVERT: R 492 ASN cc_start: 0.8477 (m-40) cc_final: 0.8013 (m-40) REVERT: S 32 PHE cc_start: 0.8248 (m-80) cc_final: 0.8017 (m-80) REVERT: S 174 LEU cc_start: 0.8623 (tp) cc_final: 0.8388 (tp) REVERT: S 202 ARG cc_start: 0.8145 (mtm110) cc_final: 0.7827 (mtm110) REVERT: S 223 ASP cc_start: 0.7921 (m-30) cc_final: 0.7494 (m-30) REVERT: S 227 TYR cc_start: 0.8417 (m-80) cc_final: 0.8137 (m-80) REVERT: B 22 ARG cc_start: 0.7280 (mtt90) cc_final: 0.6929 (mtt90) REVERT: B 42 ARG cc_start: 0.7425 (ttt-90) cc_final: 0.6965 (ttt-90) REVERT: B 44 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.6681 (mp10) REVERT: B 210 LEU cc_start: 0.8463 (tp) cc_final: 0.8047 (tp) REVERT: B 219 ARG cc_start: 0.7862 (mmt180) cc_final: 0.7525 (mmp80) REVERT: B 223 THR cc_start: 0.7775 (t) cc_final: 0.7516 (p) REVERT: B 234 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.8442 (m-80) REVERT: B 275 SER cc_start: 0.7947 (t) cc_final: 0.7709 (t) REVERT: B 317 CYS cc_start: 0.7561 (p) cc_final: 0.7333 (p) outliers start: 32 outliers final: 24 residues processed: 224 average time/residue: 0.2506 time to fit residues: 74.5351 Evaluate side-chains 233 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 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 B residue 44 GLN 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 99 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 chunk 50 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 95 optimal weight: 0.6980 chunk 109 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.130195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.111527 restraints weight = 12945.312| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.93 r_work: 0.3258 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9197 Z= 0.247 Angle : 0.581 7.498 12475 Z= 0.300 Chirality : 0.043 0.196 1411 Planarity : 0.004 0.042 1581 Dihedral : 4.536 20.450 1251 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.28 % Allowed : 18.26 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.26), residues: 1134 helix: 1.31 (0.29), residues: 352 sheet: -0.40 (0.31), residues: 272 loop : -0.99 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.004 0.001 HIS B 225 PHE 0.025 0.002 PHE S 239 TYR 0.018 0.001 TYR A 391 ARG 0.005 0.000 ARG B 52 *********************** 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: 32 poor density : 206 time to evaluate : 0.878 Fit side-chains REVERT: A 8 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7093 (mt-10) REVERT: A 216 LYS cc_start: 0.8435 (mppt) cc_final: 0.8158 (mppt) REVERT: A 231 ARG cc_start: 0.8144 (ptp90) cc_final: 0.7912 (ptp90) REVERT: A 294 GLN cc_start: 0.6944 (mm-40) cc_final: 0.6728 (mm-40) REVERT: A 327 GLU cc_start: 0.7904 (mp0) cc_final: 0.7410 (mp0) REVERT: A 374 ARG cc_start: 0.8387 (mtt-85) cc_final: 0.8138 (mtt180) REVERT: R 492 ASN cc_start: 0.8487 (m-40) cc_final: 0.8027 (m-40) REVERT: S 32 PHE cc_start: 0.8248 (m-80) cc_final: 0.7690 (m-80) REVERT: S 174 LEU cc_start: 0.8642 (tp) cc_final: 0.8409 (tp) REVERT: S 202 ARG cc_start: 0.8167 (mtm110) cc_final: 0.7855 (mtm110) REVERT: S 223 ASP cc_start: 0.7921 (m-30) cc_final: 0.7493 (m-30) REVERT: S 227 TYR cc_start: 0.8428 (m-80) cc_final: 0.8198 (m-80) REVERT: B 22 ARG cc_start: 0.7331 (mtt90) cc_final: 0.6940 (mtt90) REVERT: B 42 ARG cc_start: 0.7434 (ttt-90) cc_final: 0.6971 (ttt-90) REVERT: B 44 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.6625 (mp10) REVERT: B 219 ARG cc_start: 0.7890 (mmt180) cc_final: 0.7495 (mmp80) REVERT: B 223 THR cc_start: 0.7791 (t) cc_final: 0.7542 (p) REVERT: B 234 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8445 (m-80) REVERT: B 275 SER cc_start: 0.7955 (t) cc_final: 0.7719 (t) outliers start: 32 outliers final: 24 residues processed: 222 average time/residue: 0.2509 time to fit residues: 74.0749 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 : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 32 LYS 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 A residue 386 MET 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 155 VAL Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain B residue 44 GLN 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 25 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 109 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN B 220 GLN B 259 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 = 0.3640 r_free = 0.3640 target = 0.131249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.112600 restraints weight = 12789.847| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.91 r_work: 0.3262 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9197 Z= 0.241 Angle : 0.586 8.387 12475 Z= 0.302 Chirality : 0.043 0.201 1411 Planarity : 0.004 0.042 1581 Dihedral : 4.560 20.644 1251 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.49 % Allowed : 18.56 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.26), residues: 1134 helix: 1.27 (0.29), residues: 353 sheet: -0.40 (0.30), residues: 282 loop : -1.04 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.004 0.001 HIS B 225 PHE 0.023 0.002 PHE S 239 TYR 0.017 0.002 TYR A 391 ARG 0.005 0.000 ARG B 52 *********************** 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 242 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 0.872 Fit side-chains REVERT: A 8 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7086 (mt-10) REVERT: A 216 LYS cc_start: 0.8436 (mppt) cc_final: 0.8163 (mppt) REVERT: A 231 ARG cc_start: 0.8114 (ptp90) cc_final: 0.7894 (ptp90) REVERT: A 292 ASN cc_start: 0.8379 (t0) cc_final: 0.8133 (t0) REVERT: A 294 GLN cc_start: 0.6967 (mm-40) cc_final: 0.6744 (mm-40) REVERT: A 327 GLU cc_start: 0.7899 (mp0) cc_final: 0.7407 (mp0) REVERT: A 374 ARG cc_start: 0.8338 (mtt-85) cc_final: 0.8088 (mtt180) REVERT: R 492 ASN cc_start: 0.8482 (m-40) cc_final: 0.7998 (m-40) REVERT: S 32 PHE cc_start: 0.8266 (m-80) cc_final: 0.7708 (m-80) REVERT: S 174 LEU cc_start: 0.8646 (tp) cc_final: 0.8427 (tp) REVERT: S 202 ARG cc_start: 0.8170 (mtm110) cc_final: 0.7860 (mtm110) REVERT: S 223 ASP cc_start: 0.7902 (m-30) cc_final: 0.7475 (m-30) REVERT: S 227 TYR cc_start: 0.8419 (m-80) cc_final: 0.8185 (m-80) REVERT: B 22 ARG cc_start: 0.7364 (mtt90) cc_final: 0.6974 (mtt90) REVERT: B 42 ARG cc_start: 0.7456 (ttt-90) cc_final: 0.7005 (ttt-90) REVERT: B 44 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.6631 (mp10) REVERT: B 55 LEU cc_start: 0.8265 (mp) cc_final: 0.7966 (mp) REVERT: B 59 TYR cc_start: 0.7767 (OUTLIER) cc_final: 0.7478 (m-80) REVERT: B 219 ARG cc_start: 0.7865 (mmt180) cc_final: 0.7570 (mmp80) REVERT: B 223 THR cc_start: 0.7787 (t) cc_final: 0.7541 (p) REVERT: B 234 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.8439 (m-80) REVERT: B 275 SER cc_start: 0.7957 (t) cc_final: 0.7720 (t) outliers start: 34 outliers final: 27 residues processed: 225 average time/residue: 0.2450 time to fit residues: 73.0786 Evaluate side-chains 237 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 51 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 325 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 386 MET 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 155 VAL Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 THR 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 63 optimal weight: 0.7980 chunk 16 optimal weight: 0.0040 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 17 optimal weight: 0.0970 chunk 58 optimal weight: 0.6980 chunk 24 optimal weight: 0.0050 overall best weight: 0.2804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** 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 = 0.3675 r_free = 0.3675 target = 0.134208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.115677 restraints weight = 12835.654| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.93 r_work: 0.3313 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9197 Z= 0.147 Angle : 0.559 8.370 12475 Z= 0.286 Chirality : 0.042 0.216 1411 Planarity : 0.004 0.041 1581 Dihedral : 4.306 20.586 1251 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.67 % Allowed : 20.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.26), residues: 1134 helix: 1.36 (0.29), residues: 354 sheet: -0.33 (0.31), residues: 263 loop : -1.07 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 PHE 0.019 0.001 PHE S 239 TYR 0.012 0.001 TYR S 103 ARG 0.004 0.000 ARG B 251 ********************** 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 249 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 223 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7270 (mt-10) cc_final: 0.7048 (mt-10) REVERT: A 216 LYS cc_start: 0.8426 (mppt) cc_final: 0.8049 (mppt) REVERT: A 246 PHE cc_start: 0.8176 (t80) cc_final: 0.7956 (t80) REVERT: A 291 LEU cc_start: 0.7982 (mt) cc_final: 0.7344 (mp) REVERT: A 292 ASN cc_start: 0.8340 (t0) cc_final: 0.8109 (t0) REVERT: A 294 GLN cc_start: 0.6899 (mm-40) cc_final: 0.6677 (mm-40) REVERT: A 327 GLU cc_start: 0.7884 (mp0) cc_final: 0.7406 (mp0) REVERT: R 492 ASN cc_start: 0.8427 (m-40) cc_final: 0.8077 (m-40) REVERT: S 32 PHE cc_start: 0.8196 (m-80) cc_final: 0.7647 (m-80) REVERT: S 174 LEU cc_start: 0.8578 (tp) cc_final: 0.8378 (tp) REVERT: S 202 ARG cc_start: 0.8124 (mtm110) cc_final: 0.7888 (mtm110) REVERT: S 223 ASP cc_start: 0.7878 (m-30) cc_final: 0.7490 (m-30) REVERT: S 227 TYR cc_start: 0.8360 (m-80) cc_final: 0.8010 (m-80) REVERT: B 22 ARG cc_start: 0.7219 (mtt90) cc_final: 0.6938 (mtt90) REVERT: B 32 GLN cc_start: 0.7736 (mt0) cc_final: 0.7400 (mt0) REVERT: B 42 ARG cc_start: 0.7405 (ttt-90) cc_final: 0.6959 (ttt-90) REVERT: B 44 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.6523 (mp10) REVERT: B 55 LEU cc_start: 0.8251 (mp) cc_final: 0.8022 (mp) REVERT: B 59 TYR cc_start: 0.7488 (OUTLIER) cc_final: 0.7167 (m-80) REVERT: B 156 GLN cc_start: 0.8248 (mt0) cc_final: 0.8042 (mt0) REVERT: B 210 LEU cc_start: 0.8455 (tp) cc_final: 0.8034 (tp) REVERT: B 219 ARG cc_start: 0.7834 (mmt180) cc_final: 0.7522 (mmp80) REVERT: B 223 THR cc_start: 0.7694 (t) cc_final: 0.7429 (p) REVERT: B 234 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.8467 (m-80) REVERT: B 258 ASP cc_start: 0.8188 (t70) cc_final: 0.7846 (t70) REVERT: B 275 SER cc_start: 0.7958 (t) cc_final: 0.7724 (t) outliers start: 26 outliers final: 21 residues processed: 235 average time/residue: 0.2487 time to fit residues: 78.2845 Evaluate side-chains 238 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 356 ARG Chi-restraints excluded: chain A residue 371 ASN 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 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 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 THR 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 24 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 102 optimal weight: 0.6980 chunk 107 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 67 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN S 194 ASN 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 = 0.3662 r_free = 0.3662 target = 0.133125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.114427 restraints weight = 12826.797| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.94 r_work: 0.3298 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9197 Z= 0.180 Angle : 0.570 8.681 12475 Z= 0.291 Chirality : 0.042 0.205 1411 Planarity : 0.004 0.047 1581 Dihedral : 4.303 20.412 1251 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.56 % Allowed : 20.41 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.26), residues: 1134 helix: 1.33 (0.29), residues: 359 sheet: -0.38 (0.31), residues: 273 loop : -0.97 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 PHE 0.021 0.001 PHE B 335 TYR 0.013 0.001 TYR A 391 ARG 0.006 0.000 ARG B 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5115.21 seconds wall clock time: 91 minutes 23.42 seconds (5483.42 seconds total)