Starting phenix.real_space_refine on Wed Mar 12 13:55:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f1r_31423/03_2025/7f1r_31423.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f1r_31423/03_2025/7f1r_31423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f1r_31423/03_2025/7f1r_31423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f1r_31423/03_2025/7f1r_31423.map" model { file = "/net/cci-nas-00/data/ceres_data/7f1r_31423/03_2025/7f1r_31423.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f1r_31423/03_2025/7f1r_31423.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1639 atoms to isotropic. 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 52 5.16 5 C 4274 2.51 5 N 1110 2.21 5 O 1185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6621 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2450 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain breaks: 4 Unresolved non-hydrogen bonds: 211 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 138 Chain: "A" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1627 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2305 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 310} Chain breaks: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 78 Chain: "C" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 239 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 30} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 4.41, per 1000 atoms: 0.67 Number of scatterers: 6621 At special positions: 0 Unit cell: (114.95, 121.22, 68.97, 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 52 16.00 O 1185 8.00 N 1110 7.00 C 4274 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 10 " - pdb=" SG CYS R 34 " distance=2.03 Simple disulfide: pdb=" SG CYS R 11 " - pdb=" SG CYS R 50 " distance=2.03 Simple disulfide: pdb=" SG CYS R 28 " - pdb=" SG CYS R 267 " distance=2.03 Simple disulfide: pdb=" SG CYS R 196 " - pdb=" SG CYS R 273 " 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: 1.61 Conformation dependent library (CDL) restraints added in 1.1 seconds 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 43.2% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'R' and resid 3 through 7 Processing helix chain 'R' and resid 56 through 65 removed outlier: 4.064A pdb=" N LEU R 65 " --> pdb=" O TYR R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 153 removed outlier: 3.589A pdb=" N VAL R 146 " --> pdb=" O GLY R 142 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU R 150 " --> pdb=" O VAL R 146 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 176 removed outlier: 4.249A pdb=" N ILE R 162 " --> pdb=" O SER R 158 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR R 163 " --> pdb=" O MET R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 185 Processing helix chain 'R' and resid 193 through 226 Processing helix chain 'R' and resid 227 through 235 Processing helix chain 'R' and resid 236 through 261 Proline residue: R 257 - end of helix Processing helix chain 'R' and resid 281 through 317 removed outlier: 5.314A pdb=" N LEU R 300 " --> pdb=" O LEU R 296 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 321 through 356 removed outlier: 3.606A pdb=" N ARG R 325 " --> pdb=" O ASN R 321 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS R 326 " --> pdb=" O GLU R 322 " (cutoff:3.500A) Proline residue: R 345 - end of helix removed outlier: 3.679A pdb=" N PHE R 355 " --> pdb=" O LEU R 351 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 394 removed outlier: 4.074A pdb=" N ARG R 369 " --> pdb=" O SER R 365 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU R 370 " --> pdb=" O SER R 366 " (cutoff:3.500A) Proline residue: R 389 - end of helix Processing helix chain 'R' and resid 396 through 408 removed outlier: 3.727A pdb=" N TYR R 402 " --> pdb=" O LYS R 398 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU R 403 " --> pdb=" O PHE R 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 33 removed outlier: 3.660A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.626A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 272 through 281 removed outlier: 4.388A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.882A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 311 removed outlier: 3.697A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP A 309 " --> pdb=" O CYS A 305 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 351 removed outlier: 3.509A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.655A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 45 removed outlier: 3.557A pdb=" N ALA C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 262 through 263 removed outlier: 3.911A pdb=" N ARG R 263 " --> pdb=" O SER R 274 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER R 274 " --> pdb=" O ARG R 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.507A pdb=" N MET A 198 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.984A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.524A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 105 removed outlier: 5.910A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.433A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.349A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.629A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.860A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 975 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.97 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2094 1.35 - 1.46: 1715 1.46 - 1.58: 2883 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 6762 Sorted by residual: bond pdb=" N ARG A 313 " pdb=" CA ARG A 313 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.27e-02 6.20e+03 5.48e+00 bond pdb=" N ARG B 304 " pdb=" CA ARG B 304 " ideal model delta sigma weight residual 1.456 1.482 -0.026 1.22e-02 6.72e+03 4.43e+00 bond pdb=" CA SER R 1 " pdb=" C SER R 1 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.10e-02 2.27e+03 7.37e-01 bond pdb=" CA LEU R 128 " pdb=" C LEU R 128 " ideal model delta sigma weight residual 1.525 1.542 -0.017 2.10e-02 2.27e+03 6.53e-01 bond pdb=" C PRO R 129 " pdb=" N PRO R 130 " ideal model delta sigma weight residual 1.336 1.345 -0.009 1.20e-02 6.94e+03 5.79e-01 ... (remaining 6757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 9005 1.32 - 2.64: 158 2.64 - 3.96: 29 3.96 - 5.28: 9 5.28 - 6.60: 5 Bond angle restraints: 9206 Sorted by residual: angle pdb=" N GLN R 281 " pdb=" CA GLN R 281 " pdb=" C GLN R 281 " ideal model delta sigma weight residual 110.44 107.09 3.35 1.20e+00 6.94e-01 7.80e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 121.54 126.67 -5.13 1.91e+00 2.74e-01 7.20e+00 angle pdb=" CA ARG A 313 " pdb=" C ARG A 313 " pdb=" O ARG A 313 " ideal model delta sigma weight residual 120.54 118.15 2.39 1.04e+00 9.25e-01 5.29e+00 angle pdb=" N VAL R 178 " pdb=" CA VAL R 178 " pdb=" C VAL R 178 " ideal model delta sigma weight residual 108.88 113.21 -4.33 2.16e+00 2.14e-01 4.01e+00 angle pdb=" CA VAL R 178 " pdb=" C VAL R 178 " pdb=" N PRO R 179 " ideal model delta sigma weight residual 118.88 121.94 -3.06 1.54e+00 4.22e-01 3.95e+00 ... (remaining 9201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.64: 3652 15.64 - 31.28: 236 31.28 - 46.92: 44 46.92 - 62.55: 10 62.55 - 78.19: 5 Dihedral angle restraints: 3947 sinusoidal: 1343 harmonic: 2604 Sorted by residual: dihedral pdb=" CB CYS R 196 " pdb=" SG CYS R 196 " pdb=" SG CYS R 273 " pdb=" CB CYS R 273 " ideal model delta sinusoidal sigma weight residual -86.00 -161.48 75.48 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" CB CYS R 28 " pdb=" SG CYS R 28 " pdb=" SG CYS R 267 " pdb=" CB CYS R 267 " ideal model delta sinusoidal sigma weight residual -86.00 -35.92 -50.08 1 1.00e+01 1.00e-02 3.44e+01 dihedral pdb=" CB CYS R 11 " pdb=" SG CYS R 11 " pdb=" SG CYS R 50 " pdb=" CB CYS R 50 " ideal model delta sinusoidal sigma weight residual -86.00 -56.15 -29.85 1 1.00e+01 1.00e-02 1.27e+01 ... (remaining 3944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 643 0.025 - 0.050: 258 0.050 - 0.074: 119 0.074 - 0.099: 53 0.099 - 0.124: 25 Chirality restraints: 1098 Sorted by residual: chirality pdb=" CA LEU R 256 " pdb=" N LEU R 256 " pdb=" C LEU R 256 " pdb=" CB LEU R 256 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.58e-01 chirality pdb=" CA ARG A 313 " pdb=" N ARG A 313 " pdb=" C ARG A 313 " pdb=" CB ARG A 313 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.55e-01 ... (remaining 1095 not shown) Planarity restraints: 1148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 256 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO R 257 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO R 257 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 257 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 128 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.29e+00 pdb=" N PRO R 129 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO R 129 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 129 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 303 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.67e+00 pdb=" C ASP B 303 " -0.022 2.00e-02 2.50e+03 pdb=" O ASP B 303 " 0.008 2.00e-02 2.50e+03 pdb=" N ARG B 304 " 0.008 2.00e-02 2.50e+03 ... (remaining 1145 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1092 2.76 - 3.29: 6494 3.29 - 3.83: 11101 3.83 - 4.36: 12892 4.36 - 4.90: 22626 Nonbonded interactions: 54205 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.224 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.256 3.040 nonbonded pdb=" O LEU R 150 " pdb=" N ARG R 155 " model vdw 2.266 3.120 nonbonded pdb=" OE1 GLN B 176 " pdb=" OG1 THR B 179 " model vdw 2.279 3.040 nonbonded pdb=" O CYS A 254 " pdb=" NZ LYS A 317 " model vdw 2.321 3.120 ... (remaining 54200 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.780 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 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 : 0.002 0.030 6762 Z= 0.122 Angle : 0.484 6.596 9206 Z= 0.283 Chirality : 0.038 0.124 1098 Planarity : 0.003 0.039 1148 Dihedral : 11.209 78.194 2243 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.46 % Allowed : 1.83 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.24), residues: 872 helix: -1.30 (0.23), residues: 354 sheet: -0.71 (0.44), residues: 138 loop : -1.81 (0.26), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 339 HIS 0.002 0.000 HIS R 276 PHE 0.006 0.001 PHE B 234 TYR 0.005 0.001 TYR R 27 ARG 0.001 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 157 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 195 MET cc_start: 0.7308 (tmm) cc_final: 0.7011 (tmm) REVERT: R 369 ARG cc_start: 0.5788 (mmm-85) cc_final: 0.4496 (tpt170) REVERT: A 198 MET cc_start: 0.7252 (mpp) cc_final: 0.6982 (mpt) REVERT: A 267 PHE cc_start: 0.7686 (m-10) cc_final: 0.7310 (m-10) REVERT: A 296 TYR cc_start: 0.7637 (t80) cc_final: 0.7280 (t80) outliers start: 3 outliers final: 0 residues processed: 158 average time/residue: 0.9682 time to fit residues: 162.3698 Evaluate side-chains 111 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 265 GLN ** R 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN B 62 HIS C 44 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.171142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.132411 restraints weight = 7490.081| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.21 r_work: 0.3502 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6762 Z= 0.301 Angle : 0.662 8.050 9206 Z= 0.333 Chirality : 0.045 0.165 1098 Planarity : 0.004 0.036 1148 Dihedral : 3.729 14.090 941 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.75 % Allowed : 14.68 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.27), residues: 872 helix: 0.44 (0.27), residues: 354 sheet: -0.65 (0.39), residues: 175 loop : -1.12 (0.30), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.003 0.001 HIS B 311 PHE 0.015 0.002 PHE A 196 TYR 0.014 0.002 TYR R 203 ARG 0.008 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.769 Fit side-chains REVERT: R 195 MET cc_start: 0.7276 (tmm) cc_final: 0.6832 (tmm) REVERT: R 261 PHE cc_start: 0.7655 (m-10) cc_final: 0.7399 (m-10) REVERT: R 369 ARG cc_start: 0.6394 (mmm-85) cc_final: 0.4615 (tpt170) REVERT: R 400 ARG cc_start: 0.6424 (mtm180) cc_final: 0.6205 (mtm180) REVERT: A 14 GLU cc_start: 0.7877 (tp30) cc_final: 0.7511 (tm-30) REVERT: A 18 MET cc_start: 0.7719 (tpp) cc_final: 0.7480 (tmm) REVERT: A 24 ARG cc_start: 0.7440 (mtp-110) cc_final: 0.6733 (mtm-85) REVERT: A 296 TYR cc_start: 0.8076 (t80) cc_final: 0.7388 (t80) outliers start: 18 outliers final: 5 residues processed: 143 average time/residue: 0.9851 time to fit residues: 150.1070 Evaluate side-chains 113 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 66 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 61 optimal weight: 0.0870 chunk 85 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 227 HIS ** R 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 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 = 0.4111 r_free = 0.4111 target = 0.174435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.134793 restraints weight = 7305.972| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.15 r_work: 0.3529 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6762 Z= 0.270 Angle : 0.603 7.632 9206 Z= 0.310 Chirality : 0.043 0.154 1098 Planarity : 0.004 0.038 1148 Dihedral : 3.757 13.698 941 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.28 % Allowed : 17.89 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.28), residues: 872 helix: 1.19 (0.27), residues: 356 sheet: -0.55 (0.40), residues: 172 loop : -0.99 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS A 188 PHE 0.010 0.001 PHE R 213 TYR 0.011 0.001 TYR A 230 ARG 0.007 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: R 151 ILE cc_start: 0.5250 (OUTLIER) cc_final: 0.4770 (pp) REVERT: R 159 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7166 (tmt) REVERT: R 195 MET cc_start: 0.7406 (tmm) cc_final: 0.6868 (tmm) REVERT: R 261 PHE cc_start: 0.7794 (m-10) cc_final: 0.7493 (m-10) REVERT: R 369 ARG cc_start: 0.6371 (mmm-85) cc_final: 0.4792 (tpt170) REVERT: A 14 GLU cc_start: 0.7880 (tp30) cc_final: 0.7461 (tm-30) REVERT: A 46 LYS cc_start: 0.6674 (mptt) cc_final: 0.6273 (mptt) outliers start: 28 outliers final: 12 residues processed: 128 average time/residue: 0.9763 time to fit residues: 132.8372 Evaluate side-chains 117 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 48 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 347 ASN ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.173833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.134124 restraints weight = 7377.441| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.14 r_work: 0.3521 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6762 Z= 0.250 Angle : 0.585 8.565 9206 Z= 0.299 Chirality : 0.042 0.149 1098 Planarity : 0.004 0.038 1148 Dihedral : 3.801 14.192 941 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.89 % Allowed : 19.42 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.29), residues: 872 helix: 1.67 (0.28), residues: 349 sheet: -0.46 (0.40), residues: 177 loop : -1.10 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 99 HIS 0.004 0.001 HIS A 188 PHE 0.010 0.001 PHE A 196 TYR 0.022 0.002 TYR R 346 ARG 0.004 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: R 151 ILE cc_start: 0.5384 (OUTLIER) cc_final: 0.4931 (pp) REVERT: R 159 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7011 (tmt) REVERT: R 195 MET cc_start: 0.7373 (tmm) cc_final: 0.6705 (tmm) REVERT: R 261 PHE cc_start: 0.7930 (m-10) cc_final: 0.7435 (m-10) REVERT: R 369 ARG cc_start: 0.6425 (mmm-85) cc_final: 0.4791 (tpt170) REVERT: A 14 GLU cc_start: 0.7832 (tp30) cc_final: 0.7421 (tm-30) REVERT: B 52 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7703 (mtm-85) outliers start: 32 outliers final: 15 residues processed: 132 average time/residue: 1.0751 time to fit residues: 150.2261 Evaluate side-chains 118 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 340 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 5 optimal weight: 0.0050 chunk 62 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 347 ASN ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.175073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.136115 restraints weight = 7223.582| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.10 r_work: 0.3542 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6762 Z= 0.217 Angle : 0.598 9.728 9206 Z= 0.297 Chirality : 0.042 0.146 1098 Planarity : 0.004 0.038 1148 Dihedral : 3.863 24.778 941 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.13 % Allowed : 22.02 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.29), residues: 872 helix: 1.90 (0.28), residues: 350 sheet: -0.57 (0.41), residues: 163 loop : -1.07 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 99 HIS 0.003 0.001 HIS A 188 PHE 0.010 0.001 PHE A 196 TYR 0.018 0.001 TYR R 346 ARG 0.006 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: R 151 ILE cc_start: 0.5420 (OUTLIER) cc_final: 0.5008 (pp) REVERT: R 159 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7853 (tmt) REVERT: R 195 MET cc_start: 0.7373 (tmm) cc_final: 0.6708 (tmm) REVERT: R 369 ARG cc_start: 0.6437 (mmm-85) cc_final: 0.4769 (tpt170) REVERT: R 400 ARG cc_start: 0.6566 (mtm180) cc_final: 0.6299 (mtm-85) REVERT: A 14 GLU cc_start: 0.7798 (tp30) cc_final: 0.7378 (tm-30) REVERT: A 186 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7750 (tm-30) REVERT: B 52 ARG cc_start: 0.7921 (mtm-85) cc_final: 0.7716 (mtp85) REVERT: B 260 GLU cc_start: 0.8095 (tt0) cc_final: 0.7864 (tt0) REVERT: B 264 TYR cc_start: 0.8662 (m-80) cc_final: 0.8427 (m-10) outliers start: 27 outliers final: 16 residues processed: 126 average time/residue: 1.0820 time to fit residues: 143.9689 Evaluate side-chains 122 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 340 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 39 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 38 optimal weight: 0.0070 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 347 ASN ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.174042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.135070 restraints weight = 7272.830| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.11 r_work: 0.3531 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6762 Z= 0.220 Angle : 0.597 9.266 9206 Z= 0.296 Chirality : 0.042 0.143 1098 Planarity : 0.004 0.038 1148 Dihedral : 3.815 18.767 941 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.74 % Allowed : 22.32 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.29), residues: 872 helix: 2.05 (0.28), residues: 350 sheet: -0.51 (0.42), residues: 158 loop : -1.11 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 99 HIS 0.003 0.001 HIS B 225 PHE 0.011 0.001 PHE R 261 TYR 0.013 0.001 TYR R 163 ARG 0.007 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.772 Fit side-chains REVERT: R 151 ILE cc_start: 0.5548 (OUTLIER) cc_final: 0.5156 (pp) REVERT: R 195 MET cc_start: 0.7392 (tmm) cc_final: 0.6760 (tmm) REVERT: R 261 PHE cc_start: 0.7997 (m-80) cc_final: 0.7645 (m-80) REVERT: R 369 ARG cc_start: 0.6497 (mmm-85) cc_final: 0.4814 (tpt170) REVERT: A 14 GLU cc_start: 0.7785 (tp30) cc_final: 0.7337 (tm-30) REVERT: A 186 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7773 (tm-30) REVERT: A 198 MET cc_start: 0.8797 (mpt) cc_final: 0.8410 (mpt) REVERT: B 52 ARG cc_start: 0.7899 (mtm-85) cc_final: 0.7692 (mtp85) REVERT: B 59 TYR cc_start: 0.8788 (m-80) cc_final: 0.8310 (m-80) outliers start: 31 outliers final: 19 residues processed: 127 average time/residue: 1.0439 time to fit residues: 140.4792 Evaluate side-chains 123 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 340 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 6 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 82 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 17 optimal weight: 0.0980 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 258 ASN R 265 GLN R 347 ASN ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.170134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.131796 restraints weight = 7405.998| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.11 r_work: 0.3498 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6762 Z= 0.213 Angle : 0.600 10.686 9206 Z= 0.296 Chirality : 0.041 0.142 1098 Planarity : 0.004 0.038 1148 Dihedral : 3.819 20.917 941 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 5.20 % Allowed : 22.78 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.29), residues: 872 helix: 2.20 (0.28), residues: 345 sheet: -0.62 (0.41), residues: 165 loop : -0.99 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 99 HIS 0.003 0.001 HIS B 225 PHE 0.016 0.001 PHE R 136 TYR 0.016 0.001 TYR R 346 ARG 0.008 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.868 Fit side-chains REVERT: R 151 ILE cc_start: 0.5637 (OUTLIER) cc_final: 0.5170 (pp) REVERT: R 195 MET cc_start: 0.7277 (tmm) cc_final: 0.6674 (tmm) REVERT: R 261 PHE cc_start: 0.8055 (m-80) cc_final: 0.7682 (m-80) REVERT: R 369 ARG cc_start: 0.6532 (mmm-85) cc_final: 0.4869 (tpt170) REVERT: A 186 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7808 (tm-30) REVERT: A 198 MET cc_start: 0.8749 (mpt) cc_final: 0.8488 (mpt) REVERT: B 52 ARG cc_start: 0.7924 (mtm-85) cc_final: 0.7632 (mtp85) REVERT: B 59 TYR cc_start: 0.8773 (m-80) cc_final: 0.8317 (m-80) outliers start: 34 outliers final: 18 residues processed: 122 average time/residue: 1.0858 time to fit residues: 140.4281 Evaluate side-chains 123 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 340 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 76 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 347 ASN ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.168807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.130143 restraints weight = 7479.313| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.14 r_work: 0.3476 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6762 Z= 0.239 Angle : 0.614 11.467 9206 Z= 0.304 Chirality : 0.042 0.146 1098 Planarity : 0.004 0.038 1148 Dihedral : 3.860 21.816 941 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.28 % Allowed : 23.55 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.29), residues: 872 helix: 2.17 (0.27), residues: 346 sheet: -0.62 (0.41), residues: 165 loop : -0.96 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 99 HIS 0.003 0.001 HIS A 188 PHE 0.013 0.001 PHE R 136 TYR 0.016 0.001 TYR B 124 ARG 0.007 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.790 Fit side-chains REVERT: R 151 ILE cc_start: 0.5780 (OUTLIER) cc_final: 0.5298 (pp) REVERT: R 195 MET cc_start: 0.7285 (tmm) cc_final: 0.6701 (tmm) REVERT: R 369 ARG cc_start: 0.6620 (mmm-85) cc_final: 0.4923 (tpt170) REVERT: A 186 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7846 (tm-30) REVERT: A 198 MET cc_start: 0.8731 (mpt) cc_final: 0.8504 (mpt) REVERT: A 252 SER cc_start: 0.8715 (m) cc_final: 0.8501 (t) REVERT: B 52 ARG cc_start: 0.7924 (mtm-85) cc_final: 0.7625 (mtp85) REVERT: B 59 TYR cc_start: 0.8838 (m-80) cc_final: 0.8374 (m-80) outliers start: 28 outliers final: 21 residues processed: 120 average time/residue: 1.0888 time to fit residues: 138.6538 Evaluate side-chains 125 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 340 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 79 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 347 ASN ** R 388 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 = 0.4040 r_free = 0.4040 target = 0.167852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.128745 restraints weight = 7520.315| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.19 r_work: 0.3457 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6762 Z= 0.260 Angle : 0.630 11.975 9206 Z= 0.313 Chirality : 0.042 0.162 1098 Planarity : 0.004 0.038 1148 Dihedral : 3.876 15.433 941 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.13 % Allowed : 24.16 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.29), residues: 872 helix: 2.17 (0.27), residues: 345 sheet: -0.59 (0.40), residues: 171 loop : -0.95 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.004 0.001 HIS B 225 PHE 0.014 0.001 PHE R 136 TYR 0.027 0.002 TYR R 346 ARG 0.005 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.714 Fit side-chains REVERT: R 151 ILE cc_start: 0.5829 (OUTLIER) cc_final: 0.5384 (pp) REVERT: R 195 MET cc_start: 0.7268 (tmm) cc_final: 0.6717 (tmm) REVERT: R 369 ARG cc_start: 0.6664 (mmm-85) cc_final: 0.4984 (tpt170) REVERT: A 186 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7910 (tm-30) REVERT: A 252 SER cc_start: 0.8696 (m) cc_final: 0.8468 (t) REVERT: B 52 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.7643 (mtp85) REVERT: B 59 TYR cc_start: 0.8836 (m-80) cc_final: 0.8345 (m-80) outliers start: 27 outliers final: 19 residues processed: 123 average time/residue: 1.0663 time to fit residues: 138.8647 Evaluate side-chains 121 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 83 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 77 optimal weight: 0.0980 chunk 74 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 265 GLN R 347 ASN ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.169026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.130470 restraints weight = 7519.857| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.12 r_work: 0.3478 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6762 Z= 0.229 Angle : 0.634 11.598 9206 Z= 0.313 Chirality : 0.042 0.144 1098 Planarity : 0.004 0.038 1148 Dihedral : 3.899 17.183 941 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.67 % Allowed : 25.23 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.29), residues: 872 helix: 2.20 (0.27), residues: 343 sheet: -0.53 (0.41), residues: 169 loop : -0.86 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 99 HIS 0.004 0.001 HIS R 384 PHE 0.012 0.001 PHE R 136 TYR 0.017 0.001 TYR B 124 ARG 0.007 0.001 ARG B 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.704 Fit side-chains REVERT: R 151 ILE cc_start: 0.6055 (OUTLIER) cc_final: 0.5572 (pp) REVERT: R 195 MET cc_start: 0.7314 (tmm) cc_final: 0.6762 (tmm) REVERT: R 369 ARG cc_start: 0.6655 (mmm-85) cc_final: 0.4982 (tpt170) REVERT: A 186 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7891 (tm-30) REVERT: B 52 ARG cc_start: 0.7967 (mtm-85) cc_final: 0.7630 (mtp85) REVERT: B 59 TYR cc_start: 0.8793 (m-80) cc_final: 0.8243 (m-80) outliers start: 24 outliers final: 21 residues processed: 123 average time/residue: 1.0234 time to fit residues: 133.5193 Evaluate side-chains 126 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 340 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 31 optimal weight: 0.0270 chunk 71 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 265 GLN ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.168688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.130235 restraints weight = 7525.155| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.13 r_work: 0.3475 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.165 6762 Z= 0.361 Angle : 1.112 59.194 9206 Z= 0.621 Chirality : 0.043 0.168 1098 Planarity : 0.004 0.060 1148 Dihedral : 3.908 17.272 941 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.67 % Allowed : 24.92 % Favored : 71.41 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.29), residues: 872 helix: 2.19 (0.27), residues: 343 sheet: -0.49 (0.41), residues: 169 loop : -0.86 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 99 HIS 0.003 0.001 HIS B 183 PHE 0.010 0.001 PHE R 213 TYR 0.015 0.001 TYR B 124 ARG 0.007 0.001 ARG B 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5776.15 seconds wall clock time: 99 minutes 6.15 seconds (5946.15 seconds total)