Starting phenix.real_space_refine on Sat Dec 28 18:14:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eq1_31254/12_2024/7eq1_31254.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eq1_31254/12_2024/7eq1_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_31254/12_2024/7eq1_31254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eq1_31254/12_2024/7eq1_31254.map" model { file = "/net/cci-nas-00/data/ceres_data/7eq1_31254/12_2024/7eq1_31254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eq1_31254/12_2024/7eq1_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-5532/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: 5.44, per 1000 atoms: 0.60 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: 2.36 Conformation dependent library (CDL) restraints added in 1.1 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: 0.97 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: 2.77 Time building geometry restraints manager: 2.71 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: 0.480 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.530 Find NCS groups from input model: 0.110 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.790 ------------------------------------------------------------------------------- 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 : 1.020 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: 0.2521 time to fit residues: 65.3580 Evaluate side-chains 184 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 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 : 0.794 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6764 (mt-10) REVERT: A 9 ASP cc_start: 0.7473 (m-30) cc_final: 0.7233 (m-30) REVERT: A 207 ILE cc_start: 0.8422 (mm) cc_final: 0.8102 (mm) REVERT: A 216 LYS cc_start: 0.8237 (mppt) cc_final: 0.7882 (mppt) REVERT: A 293 LYS cc_start: 0.8186 (mtmt) cc_final: 0.7775 (mtmm) REVERT: A 327 GLU cc_start: 0.7562 (mp0) cc_final: 0.7286 (mp0) REVERT: A 356 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6801 (mtp180) REVERT: A 374 ARG cc_start: 0.8031 (mtt-85) cc_final: 0.7766 (mtt-85) REVERT: R 492 ASN cc_start: 0.8374 (m-40) cc_final: 0.7907 (m-40) REVERT: S 20 LEU cc_start: 0.8042 (mp) cc_final: 0.7837 (mp) REVERT: S 174 LEU cc_start: 0.8314 (tp) cc_final: 0.8045 (tp) REVERT: S 223 ASP cc_start: 0.7557 (m-30) cc_final: 0.7270 (m-30) REVERT: B 37 ILE cc_start: 0.8607 (mm) cc_final: 0.8376 (mm) REVERT: B 42 ARG cc_start: 0.6549 (ttt-90) cc_final: 0.6245 (ttt-90) REVERT: B 44 GLN cc_start: 0.6921 (mp-120) cc_final: 0.6369 (mp-120) REVERT: B 61 MET cc_start: 0.7438 (ptm) cc_final: 0.7215 (ptm) REVERT: B 68 ARG cc_start: 0.8105 (ttt-90) cc_final: 0.7833 (ttt180) REVERT: B 246 ASP cc_start: 0.7087 (m-30) cc_final: 0.6728 (m-30) REVERT: B 258 ASP cc_start: 0.7719 (t70) cc_final: 0.7453 (t70) REVERT: B 275 SER cc_start: 0.7577 (t) cc_final: 0.7365 (t) REVERT: B 315 VAL cc_start: 0.6891 (t) cc_final: 0.6605 (t) outliers start: 16 outliers final: 11 residues processed: 208 average time/residue: 0.2571 time to fit residues: 70.3424 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 : 0.961 ------------------------------------------------------------------------------- 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 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.0470 chunk 84 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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** ** S 142 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9197 Z= 0.189 Angle : 0.548 6.826 12475 Z= 0.286 Chirality : 0.042 0.158 1411 Planarity : 0.004 0.041 1581 Dihedral : 4.444 19.937 1251 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.33 % Allowed : 12.92 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.03 (0.29), residues: 366 sheet: -0.12 (0.30), residues: 284 loop : -1.19 (0.29), residues: 484 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 0.019 0.001 PHE S 68 TYR 0.014 0.001 TYR A 391 ARG 0.005 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 212 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 199 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8214 (mppt) cc_final: 0.7873 (mppt) REVERT: A 246 PHE cc_start: 0.7968 (t80) cc_final: 0.7751 (t80) REVERT: A 293 LYS cc_start: 0.8196 (mtmt) cc_final: 0.7823 (mtmm) REVERT: A 327 GLU cc_start: 0.7573 (mp0) cc_final: 0.7269 (mp0) REVERT: A 345 PHE cc_start: 0.7778 (m-80) cc_final: 0.7396 (m-80) REVERT: R 492 ASN cc_start: 0.8356 (m-40) cc_final: 0.7937 (m-40) REVERT: S 174 LEU cc_start: 0.8343 (tp) cc_final: 0.8091 (tp) REVERT: B 37 ILE cc_start: 0.8591 (mm) cc_final: 0.8365 (mm) REVERT: B 44 GLN cc_start: 0.6898 (mp-120) cc_final: 0.6591 (mp-120) REVERT: B 61 MET cc_start: 0.7483 (ptm) cc_final: 0.7124 (ptm) REVERT: B 68 ARG cc_start: 0.8047 (ttt-90) cc_final: 0.7762 (ttt180) REVERT: B 223 THR cc_start: 0.7510 (t) cc_final: 0.7240 (p) REVERT: B 258 ASP cc_start: 0.7732 (t70) cc_final: 0.7519 (t70) REVERT: B 315 VAL cc_start: 0.6779 (t) cc_final: 0.6480 (t) REVERT: B 317 CYS cc_start: 0.6819 (p) cc_final: 0.6476 (p) outliers start: 13 outliers final: 11 residues processed: 204 average time/residue: 0.2567 time to fit residues: 69.0720 Evaluate side-chains 209 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 198 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 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 481 LEU Chi-restraints excluded: chain B residue 135 VAL 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 76 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 11 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9197 Z= 0.180 Angle : 0.541 7.135 12475 Z= 0.280 Chirality : 0.042 0.168 1411 Planarity : 0.004 0.044 1581 Dihedral : 4.375 19.671 1251 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.46 % Allowed : 14.05 % Favored : 83.49 % 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: 1.27 (0.29), residues: 357 sheet: -0.15 (0.30), residues: 284 loop : -1.15 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 PHE 0.019 0.001 PHE S 239 TYR 0.014 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 229 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 1.049 Fit side-chains REVERT: A 9 ASP cc_start: 0.7519 (m-30) cc_final: 0.7273 (m-30) REVERT: A 246 PHE cc_start: 0.7955 (t80) cc_final: 0.7747 (t80) REVERT: A 283 ARG cc_start: 0.7953 (ttp-110) cc_final: 0.7604 (ttp80) REVERT: A 327 GLU cc_start: 0.7548 (mp0) cc_final: 0.7253 (mp0) REVERT: A 345 PHE cc_start: 0.7788 (m-80) cc_final: 0.7415 (m-80) REVERT: A 374 ARG cc_start: 0.8201 (mtt-85) cc_final: 0.7885 (mtt180) REVERT: R 492 ASN cc_start: 0.8341 (m-40) cc_final: 0.7965 (m-40) REVERT: S 174 LEU cc_start: 0.8303 (tp) cc_final: 0.8056 (tp) REVERT: B 42 ARG cc_start: 0.6634 (ttt-90) cc_final: 0.6255 (ttt-90) REVERT: B 44 GLN cc_start: 0.6906 (mp-120) cc_final: 0.5850 (mp-120) REVERT: B 61 MET cc_start: 0.7519 (ptm) cc_final: 0.7124 (ptm) REVERT: B 68 ARG cc_start: 0.8034 (ttt-90) cc_final: 0.7747 (ttt180) REVERT: B 210 LEU cc_start: 0.8348 (tp) cc_final: 0.7906 (tp) REVERT: B 219 ARG cc_start: 0.6938 (mmt180) cc_final: 0.6729 (mpt180) REVERT: B 223 THR cc_start: 0.7516 (t) cc_final: 0.7252 (p) REVERT: B 258 ASP cc_start: 0.7819 (t70) cc_final: 0.7558 (t70) REVERT: B 283 ARG cc_start: 0.8170 (tpt170) cc_final: 0.7890 (tpt170) REVERT: B 317 CYS cc_start: 0.6856 (p) cc_final: 0.6540 (p) outliers start: 24 outliers final: 14 residues processed: 217 average time/residue: 0.2643 time to fit residues: 75.5929 Evaluate side-chains 210 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 196 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain 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 S residue 93 MET Chi-restraints excluded: chain B residue 135 VAL 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 61 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 0.6980 chunk 55 optimal weight: 0.4980 chunk 97 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.1516 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= 0.230 Angle : 0.557 6.352 12475 Z= 0.290 Chirality : 0.043 0.177 1411 Planarity : 0.004 0.044 1581 Dihedral : 4.475 19.858 1251 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.36 % Allowed : 16.41 % Favored : 81.23 % 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: 1.27 (0.28), residues: 357 sheet: -0.16 (0.30), residues: 281 loop : -1.12 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS A 362 PHE 0.022 0.002 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 230 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 1.076 Fit side-chains REVERT: A 9 ASP cc_start: 0.7518 (m-30) cc_final: 0.7297 (m-30) REVERT: A 216 LYS cc_start: 0.8178 (mppt) cc_final: 0.7879 (mppt) REVERT: A 283 ARG cc_start: 0.7907 (ttp-110) cc_final: 0.7487 (ttp80) REVERT: A 292 ASN cc_start: 0.8152 (t0) cc_final: 0.7790 (t0) REVERT: A 327 GLU cc_start: 0.7553 (mp0) cc_final: 0.7219 (mp0) REVERT: A 345 PHE cc_start: 0.7797 (m-80) cc_final: 0.7418 (m-80) REVERT: A 356 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.6668 (mtp180) REVERT: R 492 ASN cc_start: 0.8372 (m-40) cc_final: 0.7941 (m-40) REVERT: S 174 LEU cc_start: 0.8399 (tp) cc_final: 0.8151 (tp) REVERT: B 32 GLN cc_start: 0.7772 (mt0) cc_final: 0.7489 (mt0) REVERT: B 42 ARG cc_start: 0.6604 (ttt-90) cc_final: 0.6258 (ttt-90) REVERT: B 44 GLN cc_start: 0.6939 (mp-120) cc_final: 0.5794 (mp-120) REVERT: B 59 TYR cc_start: 0.7196 (OUTLIER) cc_final: 0.6885 (m-10) REVERT: B 61 MET cc_start: 0.7581 (ptm) cc_final: 0.7155 (ptm) REVERT: B 223 THR cc_start: 0.7569 (t) cc_final: 0.7310 (p) REVERT: B 258 ASP cc_start: 0.7778 (t70) cc_final: 0.7434 (t70) REVERT: B 275 SER cc_start: 0.7564 (t) cc_final: 0.7317 (t) REVERT: B 317 CYS cc_start: 0.6865 (p) cc_final: 0.6549 (p) outliers start: 23 outliers final: 18 residues processed: 216 average time/residue: 0.2652 time to fit residues: 75.1487 Evaluate side-chains 223 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 282 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 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 463 THR Chi-restraints excluded: chain R residue 464 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL 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 97 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.0870 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN S 232 HIS ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.1631 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= 0.208 Angle : 0.552 6.726 12475 Z= 0.285 Chirality : 0.042 0.183 1411 Planarity : 0.004 0.044 1581 Dihedral : 4.454 19.925 1251 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.67 % Allowed : 17.54 % Favored : 79.79 % 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: 1.32 (0.29), residues: 357 sheet: -0.22 (0.31), residues: 274 loop : -1.06 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 PHE 0.026 0.001 PHE S 68 TYR 0.016 0.001 TYR A 391 ARG 0.003 0.000 ARG B 251 *********************** 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 229 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 1.059 Fit side-chains REVERT: A 9 ASP cc_start: 0.7520 (m-30) cc_final: 0.7284 (m-30) REVERT: A 216 LYS cc_start: 0.8169 (mppt) cc_final: 0.7862 (mppt) REVERT: A 283 ARG cc_start: 0.7956 (ttp-110) cc_final: 0.7646 (ttp80) REVERT: A 292 ASN cc_start: 0.8108 (t0) cc_final: 0.7706 (t0) REVERT: A 327 GLU cc_start: 0.7548 (mp0) cc_final: 0.7209 (mp0) REVERT: A 345 PHE cc_start: 0.7819 (m-80) cc_final: 0.7468 (m-80) REVERT: R 492 ASN cc_start: 0.8356 (m-40) cc_final: 0.7954 (m-40) REVERT: S 32 PHE cc_start: 0.7868 (m-80) cc_final: 0.7483 (m-80) REVERT: S 174 LEU cc_start: 0.8398 (tp) cc_final: 0.8134 (tp) REVERT: B 42 ARG cc_start: 0.6601 (ttt-90) cc_final: 0.6310 (ttt-90) REVERT: B 44 GLN cc_start: 0.6963 (mp-120) cc_final: 0.5910 (mp-120) REVERT: B 59 TYR cc_start: 0.7209 (OUTLIER) cc_final: 0.6991 (m-10) REVERT: B 61 MET cc_start: 0.7588 (ptm) cc_final: 0.7330 (ptm) REVERT: B 68 ARG cc_start: 0.8073 (ttt-90) cc_final: 0.7761 (ttt180) REVERT: B 223 THR cc_start: 0.7549 (t) cc_final: 0.7299 (p) REVERT: B 258 ASP cc_start: 0.7817 (t70) cc_final: 0.7448 (t70) outliers start: 26 outliers final: 20 residues processed: 214 average time/residue: 0.2624 time to fit residues: 74.1025 Evaluate side-chains 224 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 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 463 THR Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain R residue 508 CYS Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 107 optimal weight: 0.0770 chunk 67 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.1715 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= 0.182 Angle : 0.546 6.786 12475 Z= 0.281 Chirality : 0.042 0.195 1411 Planarity : 0.004 0.044 1581 Dihedral : 4.381 19.872 1251 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.28 % Allowed : 17.54 % Favored : 79.18 % 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: -0.13 (0.26), residues: 1134 helix: 1.38 (0.29), residues: 357 sheet: -0.27 (0.31), residues: 276 loop : -1.02 (0.29), residues: 501 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 68 TYR 0.014 0.001 TYR A 391 ARG 0.003 0.000 ARG A 356 *********************** 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 : 1.135 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7504 (m-30) cc_final: 0.7248 (m-30) REVERT: A 216 LYS cc_start: 0.8165 (mppt) cc_final: 0.7859 (mppt) REVERT: A 231 ARG cc_start: 0.8065 (ptp90) cc_final: 0.7834 (ptp90) REVERT: A 283 ARG cc_start: 0.7848 (ttp-110) cc_final: 0.7626 (ttp80) REVERT: A 327 GLU cc_start: 0.7526 (mp0) cc_final: 0.7174 (mp0) REVERT: A 345 PHE cc_start: 0.7840 (m-80) cc_final: 0.7490 (m-80) REVERT: A 374 ARG cc_start: 0.8128 (mtt-85) cc_final: 0.7827 (mtt180) REVERT: R 492 ASN cc_start: 0.8342 (m-40) cc_final: 0.7944 (m-40) REVERT: S 32 PHE cc_start: 0.7859 (m-80) cc_final: 0.7562 (m-80) REVERT: S 174 LEU cc_start: 0.8308 (tp) cc_final: 0.8086 (tp) REVERT: B 42 ARG cc_start: 0.6609 (ttt-90) cc_final: 0.6319 (ttt-90) REVERT: B 44 GLN cc_start: 0.6961 (mp-120) cc_final: 0.5924 (mp-120) REVERT: B 55 LEU cc_start: 0.8131 (mp) cc_final: 0.7899 (mp) REVERT: B 59 TYR cc_start: 0.7198 (OUTLIER) cc_final: 0.6982 (m-10) REVERT: B 61 MET cc_start: 0.7596 (ptm) cc_final: 0.7219 (ptm) REVERT: B 68 ARG cc_start: 0.8037 (ttt-90) cc_final: 0.7718 (ttt180) REVERT: B 100 VAL cc_start: 0.8290 (OUTLIER) cc_final: 0.8076 (p) REVERT: B 223 THR cc_start: 0.7527 (t) cc_final: 0.7276 (p) REVERT: B 258 ASP cc_start: 0.7822 (t70) cc_final: 0.7481 (t70) REVERT: B 317 CYS cc_start: 0.6793 (p) cc_final: 0.6467 (p) outliers start: 32 outliers final: 24 residues processed: 224 average time/residue: 0.2806 time to fit residues: 83.2954 Evaluate side-chains 229 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 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 S residue 193 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL 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 64 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.1790 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= 0.277 Angle : 0.597 7.600 12475 Z= 0.308 Chirality : 0.043 0.185 1411 Planarity : 0.004 0.042 1581 Dihedral : 4.595 20.639 1251 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.49 % Allowed : 18.15 % Favored : 78.36 % 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: -0.30 (0.26), residues: 1134 helix: 1.09 (0.28), residues: 362 sheet: -0.42 (0.31), residues: 272 loop : -0.97 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS B 225 PHE 0.021 0.002 PHE S 68 TYR 0.019 0.002 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 243 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 1.029 Fit side-chains REVERT: A 9 ASP cc_start: 0.7511 (m-30) cc_final: 0.7278 (m-30) REVERT: A 216 LYS cc_start: 0.8177 (mppt) cc_final: 0.7968 (mppt) REVERT: A 231 ARG cc_start: 0.8091 (ptp90) cc_final: 0.7855 (ptp90) REVERT: A 292 ASN cc_start: 0.8205 (t0) cc_final: 0.7897 (t0) REVERT: A 294 GLN cc_start: 0.6547 (mm-40) cc_final: 0.6332 (mm-40) REVERT: A 327 GLU cc_start: 0.7552 (mp0) cc_final: 0.7158 (mp0) REVERT: A 370 GLU cc_start: 0.7368 (pp20) cc_final: 0.7062 (pp20) REVERT: A 374 ARG cc_start: 0.8229 (mtt-85) cc_final: 0.7936 (mtt180) REVERT: R 492 ASN cc_start: 0.8394 (m-40) cc_final: 0.7954 (m-40) REVERT: S 32 PHE cc_start: 0.7877 (m-80) cc_final: 0.7577 (m-80) REVERT: S 174 LEU cc_start: 0.8446 (tp) cc_final: 0.8182 (tp) REVERT: B 44 GLN cc_start: 0.6974 (mp-120) cc_final: 0.6769 (mp-120) REVERT: B 47 THR cc_start: 0.8031 (m) cc_final: 0.7752 (p) REVERT: B 68 ARG cc_start: 0.8104 (ttt-90) cc_final: 0.7828 (ttt180) REVERT: B 100 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.8112 (p) REVERT: B 223 THR cc_start: 0.7689 (t) cc_final: 0.7438 (p) REVERT: B 258 ASP cc_start: 0.7863 (t70) cc_final: 0.7111 (t0) REVERT: B 275 SER cc_start: 0.7612 (t) cc_final: 0.7359 (t) REVERT: B 317 CYS cc_start: 0.6793 (p) cc_final: 0.6492 (p) outliers start: 34 outliers final: 25 residues processed: 228 average time/residue: 0.2499 time to fit residues: 75.5549 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 : 1.014 ------------------------------------------------------------------------------- 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 335 THR Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 304 PHE Chi-restraints excluded: chain R residue 347 TYR Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 386 ILE Chi-restraints excluded: chain R residue 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 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL 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 94 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 103 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 0.0270 chunk 90 optimal weight: 0.6980 chunk 95 optimal weight: 0.1980 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.4038 ------------------------------------------------------------------------------- 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 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.1897 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= 0.163 Angle : 0.563 8.119 12475 Z= 0.288 Chirality : 0.042 0.191 1411 Planarity : 0.004 0.042 1581 Dihedral : 4.371 20.051 1251 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.77 % Allowed : 19.90 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.19 (0.26), residues: 1134 helix: 1.41 (0.29), residues: 348 sheet: -0.36 (0.31), residues: 263 loop : -1.03 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 PHE 0.016 0.001 PHE S 68 TYR 0.012 0.001 TYR R 381 ARG 0.007 0.000 ARG B 22 *********************** 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 238 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7487 (m-30) cc_final: 0.7245 (m-30) REVERT: A 216 LYS cc_start: 0.8165 (mppt) cc_final: 0.7950 (mppt) REVERT: A 231 ARG cc_start: 0.7935 (ptp90) cc_final: 0.7711 (ptp90) REVERT: A 292 ASN cc_start: 0.8159 (t0) cc_final: 0.7840 (t0) REVERT: A 294 GLN cc_start: 0.6531 (mm-40) cc_final: 0.6315 (mm-40) REVERT: A 327 GLU cc_start: 0.7512 (mp0) cc_final: 0.7144 (mp0) REVERT: A 374 ARG cc_start: 0.8131 (mtt-85) cc_final: 0.7889 (mtt-85) REVERT: R 492 ASN cc_start: 0.8322 (m-40) cc_final: 0.7972 (m-40) REVERT: S 174 LEU cc_start: 0.8338 (tp) cc_final: 0.8102 (tp) REVERT: S 202 ARG cc_start: 0.8103 (mtm110) cc_final: 0.7751 (mtm180) REVERT: B 22 ARG cc_start: 0.7202 (mtt90) cc_final: 0.6856 (mpt90) REVERT: B 32 GLN cc_start: 0.7686 (mt0) cc_final: 0.7372 (mt0) REVERT: B 44 GLN cc_start: 0.6955 (mp-120) cc_final: 0.6755 (mp-120) REVERT: B 47 THR cc_start: 0.8004 (m) cc_final: 0.7649 (p) REVERT: B 55 LEU cc_start: 0.8118 (mp) cc_final: 0.7859 (mp) REVERT: B 68 ARG cc_start: 0.7999 (ttt-90) cc_final: 0.7658 (ttt180) REVERT: B 100 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.8084 (p) REVERT: B 156 GLN cc_start: 0.8076 (mt0) cc_final: 0.7868 (mt0) REVERT: B 210 LEU cc_start: 0.8348 (tp) cc_final: 0.7913 (tp) REVERT: B 223 THR cc_start: 0.7529 (t) cc_final: 0.7258 (p) REVERT: B 258 ASP cc_start: 0.7907 (t70) cc_final: 0.7179 (t0) REVERT: B 283 ARG cc_start: 0.8230 (tpt170) cc_final: 0.7947 (tpt170) REVERT: B 317 CYS cc_start: 0.6749 (p) cc_final: 0.6431 (p) outliers start: 27 outliers final: 23 residues processed: 225 average time/residue: 0.2675 time to fit residues: 79.4396 Evaluate side-chains 234 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 210 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 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 356 ARG Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 304 PHE Chi-restraints excluded: chain R residue 347 TYR Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 386 ILE Chi-restraints excluded: chain R residue 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 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL 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 64 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 0.3980 chunk 54 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.1890 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= 0.201 Angle : 0.573 8.634 12475 Z= 0.293 Chirality : 0.042 0.193 1411 Planarity : 0.004 0.038 1581 Dihedral : 4.411 19.834 1251 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.56 % Allowed : 19.18 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.19 (0.26), residues: 1134 helix: 1.33 (0.29), residues: 353 sheet: -0.38 (0.30), residues: 282 loop : -1.00 (0.29), residues: 499 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 0.013 0.001 PHE S 32 TYR 0.015 0.001 TYR A 391 ARG 0.006 0.000 ARG B 22 ********************** 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 236 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 211 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7490 (m-30) cc_final: 0.7232 (m-30) REVERT: A 10 LYS cc_start: 0.7790 (mttt) cc_final: 0.7463 (ttmm) REVERT: A 216 LYS cc_start: 0.8166 (mppt) cc_final: 0.7946 (mppt) REVERT: A 231 ARG cc_start: 0.7938 (ptp90) cc_final: 0.7716 (ptp90) REVERT: A 292 ASN cc_start: 0.8184 (t0) cc_final: 0.7841 (t0) REVERT: A 294 GLN cc_start: 0.6510 (mm-40) cc_final: 0.6306 (mm-40) REVERT: A 327 GLU cc_start: 0.7503 (mp0) cc_final: 0.7127 (mp0) REVERT: A 374 ARG cc_start: 0.8236 (mtt-85) cc_final: 0.7957 (mtt180) REVERT: A 380 ARG cc_start: 0.7451 (ttt90) cc_final: 0.7109 (ttt180) REVERT: R 492 ASN cc_start: 0.8371 (m-40) cc_final: 0.7982 (m-40) REVERT: S 174 LEU cc_start: 0.8350 (tp) cc_final: 0.8127 (tp) REVERT: B 22 ARG cc_start: 0.7241 (mtt90) cc_final: 0.6925 (mpt90) REVERT: B 47 THR cc_start: 0.8022 (m) cc_final: 0.7671 (p) REVERT: B 68 ARG cc_start: 0.8047 (ttt-90) cc_final: 0.7740 (ttt180) REVERT: B 223 THR cc_start: 0.7530 (t) cc_final: 0.7270 (p) REVERT: B 258 ASP cc_start: 0.7894 (t70) cc_final: 0.7292 (t0) REVERT: B 275 SER cc_start: 0.7601 (t) cc_final: 0.7348 (t) outliers start: 25 outliers final: 24 residues processed: 224 average time/residue: 0.2545 time to fit residues: 75.7470 Evaluate side-chains 236 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 212 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 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 356 ARG Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 304 PHE Chi-restraints excluded: chain R residue 347 TYR Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 386 ILE Chi-restraints excluded: chain R residue 423 THR Chi-restraints excluded: chain R residue 463 THR Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain R residue 508 CYS Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL 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 27 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.0570 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** 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 = 0.132567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.113829 restraints weight = 12605.056| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.96 r_work: 0.3280 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 9197 Z= 0.253 Angle : 0.902 59.168 12475 Z= 0.505 Chirality : 0.043 0.301 1411 Planarity : 0.004 0.077 1581 Dihedral : 4.441 19.824 1251 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.67 % Allowed : 19.49 % Favored : 77.85 % 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: 1.33 (0.29), residues: 353 sheet: -0.39 (0.30), residues: 282 loop : -0.99 (0.29), residues: 499 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 0.019 0.002 PHE S 239 TYR 0.015 0.001 TYR A 391 ARG 0.020 0.001 ARG B 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2463.39 seconds wall clock time: 45 minutes 15.33 seconds (2715.33 seconds total)