Starting phenix.real_space_refine on Tue Apr 29 13:45:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f1q_31422/04_2025/7f1q_31422.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f1q_31422/04_2025/7f1q_31422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f1q_31422/04_2025/7f1q_31422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f1q_31422/04_2025/7f1q_31422.map" model { file = "/net/cci-nas-00/data/ceres_data/7f1q_31422/04_2025/7f1q_31422.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f1q_31422/04_2025/7f1q_31422.cif" } resolution = 2.9 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= 0.005 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 1938 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 55 5.16 5 C 4588 2.51 5 N 1198 2.21 5 O 1282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7123 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2864 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 353} Chain breaks: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1646 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'TYR:plan': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2370 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 314} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 61 Chain: "C" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 243 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 30} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 4.74, per 1000 atoms: 0.67 Number of scatterers: 7123 At special positions: 0 Unit cell: (119.13, 128.535, 76.285, 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 55 16.00 O 1282 8.00 N 1198 7.00 C 4588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, 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 15 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 116 " - pdb=" SG CYS R 365 " distance=2.04 Simple disulfide: pdb=" SG CYS R 197 " - pdb=" SG CYS R 274 " distance=2.03 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: 1.81 Conformation dependent library (CDL) restraints added in 1.0 seconds 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1778 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 11 sheets defined 44.6% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'R' and resid 2 through 6 removed outlier: 4.547A pdb=" N THR R 6 " --> pdb=" O ALA R 3 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 69 removed outlier: 3.912A pdb=" N LYS R 60 " --> pdb=" O GLU R 56 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU R 66 " --> pdb=" O VAL R 62 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA R 69 " --> pdb=" O LEU R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 129 removed outlier: 3.728A pdb=" N LYS R 122 " --> pdb=" O LYS R 118 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU R 128 " --> pdb=" O ILE R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 154 Processing helix chain 'R' and resid 159 through 188 Proline residue: R 180 - end of helix removed outlier: 3.766A pdb=" N ALA R 187 " --> pdb=" O ALA R 183 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA R 188 " --> pdb=" O HIS R 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 228 Processing helix chain 'R' and resid 228 through 236 removed outlier: 4.252A pdb=" N LYS R 234 " --> pdb=" O VAL R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 262 Proline residue: R 258 - end of helix Processing helix chain 'R' and resid 282 through 297 removed outlier: 3.589A pdb=" N VAL R 295 " --> pdb=" O THR R 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 317 removed outlier: 4.104A pdb=" N SER R 311 " --> pdb=" O VAL R 307 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY R 312 " --> pdb=" O ILE R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 318 through 320 No H-bonds generated for 'chain 'R' and resid 318 through 320' Processing helix chain 'R' and resid 322 through 356 removed outlier: 3.678A pdb=" N ARG R 328 " --> pdb=" O LYS R 324 " (cutoff:3.500A) Proline residue: R 346 - end of helix Processing helix chain 'R' and resid 364 through 394 Proline residue: R 390 - end of helix Processing helix chain 'R' and resid 397 through 409 Processing helix chain 'A' and resid 7 through 33 Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.054A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.736A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.798A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.695A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'R' and resid 9 through 10 removed outlier: 3.927A pdb=" N CYS R 10 " --> pdb=" O CYS R 116 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N CYS R 116 " --> pdb=" O CYS R 10 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'R' and resid 26 through 29 Processing sheet with id=AA3, first strand: chain 'R' and resid 264 through 268 removed outlier: 3.505A pdb=" N HIS R 271 " --> pdb=" O GLU R 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 190 removed outlier: 4.081A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.705A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.682A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.202A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.813A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.900A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.785A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.715A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 383 hydrogen bonds defined for protein. 1101 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: 2.30 Time building geometry restraints manager: 2.12 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: 2268 1.35 - 1.46: 1827 1.46 - 1.58: 3111 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 7279 Sorted by residual: bond pdb=" N TYR R 347 " pdb=" CA TYR R 347 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.71e+00 bond pdb=" N PHE R 360 " pdb=" CA PHE R 360 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.42e-02 4.96e+03 5.71e+00 bond pdb=" N LYS R 60 " pdb=" CA LYS R 60 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.21e-02 6.83e+03 5.16e+00 bond pdb=" N PHE R 359 " pdb=" CA PHE R 359 " ideal model delta sigma weight residual 1.456 1.482 -0.026 1.22e-02 6.72e+03 4.65e+00 bond pdb=" C PHE R 360 " pdb=" O PHE R 360 " ideal model delta sigma weight residual 1.231 1.244 -0.013 1.16e-02 7.43e+03 1.28e+00 ... (remaining 7274 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 9612 1.34 - 2.68: 228 2.68 - 4.02: 38 4.02 - 5.35: 16 5.35 - 6.69: 9 Bond angle restraints: 9903 Sorted by residual: angle pdb=" CA PHE R 360 " pdb=" CB PHE R 360 " pdb=" CG PHE R 360 " ideal model delta sigma weight residual 113.80 118.62 -4.82 1.00e+00 1.00e+00 2.32e+01 angle pdb=" CA PHE R 359 " pdb=" C PHE R 359 " pdb=" O PHE R 359 " ideal model delta sigma weight residual 121.16 116.37 4.79 1.12e+00 7.97e-01 1.83e+01 angle pdb=" N PHE R 359 " pdb=" CA PHE R 359 " pdb=" C PHE R 359 " ideal model delta sigma weight residual 110.28 104.61 5.67 1.48e+00 4.57e-01 1.47e+01 angle pdb=" C ARG R 127 " pdb=" N LEU R 128 " pdb=" CA LEU R 128 " ideal model delta sigma weight residual 123.04 117.89 5.15 1.59e+00 3.96e-01 1.05e+01 angle pdb=" C VAL R 179 " pdb=" CA VAL R 179 " pdb=" CB VAL R 179 " ideal model delta sigma weight residual 113.70 110.70 3.00 9.50e-01 1.11e+00 9.97e+00 ... (remaining 9898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 3981 17.55 - 35.10: 234 35.10 - 52.66: 40 52.66 - 70.21: 10 70.21 - 87.76: 6 Dihedral angle restraints: 4271 sinusoidal: 1533 harmonic: 2738 Sorted by residual: dihedral pdb=" CB CYS R 15 " pdb=" SG CYS R 15 " pdb=" SG CYS R 112 " pdb=" CB CYS R 112 " ideal model delta sinusoidal sigma weight residual 93.00 150.49 -57.49 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CA LEU R 128 " pdb=" C LEU R 128 " pdb=" N LEU R 129 " pdb=" CA LEU R 129 " ideal model delta harmonic sigma weight residual 180.00 150.40 29.60 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CB CYS R 116 " pdb=" SG CYS R 116 " pdb=" SG CYS R 365 " pdb=" CB CYS R 365 " ideal model delta sinusoidal sigma weight residual -86.00 -40.12 -45.88 1 1.00e+01 1.00e-02 2.92e+01 ... (remaining 4268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1041 0.060 - 0.120: 118 0.120 - 0.180: 5 0.180 - 0.240: 0 0.240 - 0.300: 2 Chirality restraints: 1166 Sorted by residual: chirality pdb=" CA PHE R 359 " pdb=" N PHE R 359 " pdb=" C PHE R 359 " pdb=" CB PHE R 359 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA PHE R 360 " pdb=" N PHE R 360 " pdb=" C PHE R 360 " pdb=" CB PHE R 360 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ILE A 184 " pdb=" N ILE A 184 " pdb=" C ILE A 184 " pdb=" CB ILE A 184 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 1163 not shown) Planarity restraints: 1241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 359 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.20e+00 pdb=" C PHE R 359 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE R 359 " 0.009 2.00e-02 2.50e+03 pdb=" N PHE R 360 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN R 290 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C GLN R 290 " -0.023 2.00e-02 2.50e+03 pdb=" O GLN R 290 " 0.009 2.00e-02 2.50e+03 pdb=" N THR R 291 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 257 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO R 258 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO R 258 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 258 " -0.019 5.00e-02 4.00e+02 ... (remaining 1238 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1719 2.79 - 3.32: 6898 3.32 - 3.85: 12255 3.85 - 4.37: 14137 4.37 - 4.90: 24602 Nonbonded interactions: 59611 Sorted by model distance: nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.271 3.040 nonbonded pdb=" O CYS R 386 " pdb=" ND2 ASN R 389 " model vdw 2.306 3.120 nonbonded pdb=" OG1 THR R 161 " pdb=" OD2 ASP R 221 " model vdw 2.314 3.040 nonbonded pdb=" NE2 GLN B 75 " pdb=" O VAL B 100 " model vdw 2.319 3.120 ... (remaining 59606 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.160 Find NCS groups from input model: 0.100 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:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 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 0.034 7284 Z= 0.127 Angle : 0.549 6.692 9913 Z= 0.327 Chirality : 0.039 0.300 1166 Planarity : 0.003 0.033 1241 Dihedral : 12.031 87.760 2478 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.27 % Allowed : 2.71 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.24), residues: 924 helix: -0.33 (0.24), residues: 381 sheet: -0.72 (0.34), residues: 188 loop : -1.80 (0.27), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 169 HIS 0.002 0.000 HIS B 311 PHE 0.008 0.001 PHE A 354 TYR 0.009 0.001 TYR R 347 ARG 0.001 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.15087 ( 383) hydrogen bonds : angle 5.96146 ( 1101) SS BOND : bond 0.00330 ( 5) SS BOND : angle 0.68199 ( 10) covalent geometry : bond 0.00211 ( 7279) covalent geometry : angle 0.54933 ( 9903) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 0.775 Fit side-chains REVERT: R 230 VAL cc_start: 0.8474 (m) cc_final: 0.8082 (t) outliers start: 2 outliers final: 0 residues processed: 172 average time/residue: 0.9872 time to fit residues: 182.1092 Evaluate side-chains 114 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 18 GLN R 184 HIS R 266 GLN R 271 HIS R 277 HIS A 255 ASN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 266 HIS C 44 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.152379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.117659 restraints weight = 8264.087| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.04 r_work: 0.3206 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 7284 Z= 0.307 Angle : 0.704 8.606 9913 Z= 0.371 Chirality : 0.047 0.230 1166 Planarity : 0.004 0.034 1241 Dihedral : 4.538 24.513 995 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.48 % Allowed : 13.03 % Favored : 82.50 % 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: -0.47 (0.26), residues: 924 helix: 0.48 (0.25), residues: 386 sheet: -0.53 (0.34), residues: 208 loop : -0.95 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP R 182 HIS 0.007 0.002 HIS R 271 PHE 0.024 0.003 PHE R 214 TYR 0.019 0.002 TYR B 105 ARG 0.007 0.001 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.04886 ( 383) hydrogen bonds : angle 5.19242 ( 1101) SS BOND : bond 0.01256 ( 5) SS BOND : angle 2.20147 ( 10) covalent geometry : bond 0.00706 ( 7279) covalent geometry : angle 0.70078 ( 9903) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.749 Fit side-chains REVERT: R 178 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8886 (t) REVERT: R 280 TYR cc_start: 0.8626 (p90) cc_final: 0.8265 (p90) REVERT: R 290 GLN cc_start: 0.8544 (tm-30) cc_final: 0.7579 (tp40) REVERT: R 325 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.6921 (mptm) REVERT: R 359 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7866 (t80) REVERT: A 20 ASP cc_start: 0.7584 (m-30) cc_final: 0.7274 (m-30) REVERT: A 216 GLU cc_start: 0.8697 (tt0) cc_final: 0.8469 (tt0) REVERT: A 306 GLN cc_start: 0.7187 (tp40) cc_final: 0.6850 (mm-40) REVERT: A 308 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7828 (mp0) REVERT: A 350 ASP cc_start: 0.7603 (m-30) cc_final: 0.7245 (m-30) REVERT: B 52 ARG cc_start: 0.8225 (mtt-85) cc_final: 0.7819 (ptp90) REVERT: B 268 ASN cc_start: 0.8281 (m110) cc_final: 0.7822 (t0) REVERT: B 280 LYS cc_start: 0.8210 (tptt) cc_final: 0.7996 (tmtm) outliers start: 33 outliers final: 16 residues processed: 157 average time/residue: 1.0788 time to fit residues: 180.3831 Evaluate side-chains 135 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 325 LYS Chi-restraints excluded: chain R residue 359 PHE Chi-restraints excluded: chain R residue 386 CYS Chi-restraints excluded: chain R residue 387 CYS Chi-restraints excluded: chain R residue 391 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 54 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 18 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 266 GLN R 271 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.155470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.121588 restraints weight = 8221.205| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.03 r_work: 0.3242 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7284 Z= 0.148 Angle : 0.558 9.749 9913 Z= 0.288 Chirality : 0.041 0.212 1166 Planarity : 0.003 0.033 1241 Dihedral : 4.156 25.724 995 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.61 % Allowed : 16.28 % Favored : 79.10 % 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: 0.07 (0.27), residues: 924 helix: 1.09 (0.26), residues: 386 sheet: -0.45 (0.35), residues: 200 loop : -0.74 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 182 HIS 0.004 0.001 HIS B 142 PHE 0.012 0.001 PHE R 175 TYR 0.007 0.001 TYR R 61 ARG 0.005 0.001 ARG R 319 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 383) hydrogen bonds : angle 4.92603 ( 1101) SS BOND : bond 0.00553 ( 5) SS BOND : angle 1.95973 ( 10) covalent geometry : bond 0.00336 ( 7279) covalent geometry : angle 0.55449 ( 9903) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 0.812 Fit side-chains REVERT: R 120 ASN cc_start: 0.7716 (m110) cc_final: 0.7511 (m-40) REVERT: R 290 GLN cc_start: 0.8514 (tm-30) cc_final: 0.7735 (tp40) REVERT: R 334 PHE cc_start: 0.7786 (m-10) cc_final: 0.7470 (m-80) REVERT: R 359 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7818 (t80) REVERT: A 216 GLU cc_start: 0.8587 (tt0) cc_final: 0.8334 (tt0) REVERT: A 308 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: A 350 ASP cc_start: 0.7644 (m-30) cc_final: 0.7288 (m-30) REVERT: B 52 ARG cc_start: 0.8169 (mtt-85) cc_final: 0.7710 (ptp90) REVERT: B 188 MET cc_start: 0.8188 (mmm) cc_final: 0.7891 (mmm) REVERT: B 249 THR cc_start: 0.8338 (OUTLIER) cc_final: 0.8012 (m) REVERT: B 268 ASN cc_start: 0.8382 (m110) cc_final: 0.7780 (t0) REVERT: B 280 LYS cc_start: 0.8221 (tptt) cc_final: 0.7976 (tmtm) outliers start: 34 outliers final: 12 residues processed: 139 average time/residue: 0.9239 time to fit residues: 137.4450 Evaluate side-chains 124 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 359 PHE Chi-restraints excluded: chain R residue 386 CYS Chi-restraints excluded: chain R residue 387 CYS Chi-restraints excluded: chain R residue 391 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 78 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 271 HIS ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** 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 = 0.3710 r_free = 0.3710 target = 0.147003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.110670 restraints weight = 8283.514| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.22 r_work: 0.3139 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 7284 Z= 0.284 Angle : 0.671 8.732 9913 Z= 0.352 Chirality : 0.046 0.224 1166 Planarity : 0.004 0.031 1241 Dihedral : 4.461 25.214 995 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.83 % Allowed : 16.01 % Favored : 78.15 % 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: -0.07 (0.27), residues: 924 helix: 0.97 (0.26), residues: 386 sheet: -0.74 (0.32), residues: 229 loop : -0.61 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 182 HIS 0.007 0.001 HIS B 142 PHE 0.019 0.002 PHE R 214 TYR 0.021 0.002 TYR B 59 ARG 0.007 0.001 ARG R 328 Details of bonding type rmsd hydrogen bonds : bond 0.04494 ( 383) hydrogen bonds : angle 5.30096 ( 1101) SS BOND : bond 0.00507 ( 5) SS BOND : angle 2.65440 ( 10) covalent geometry : bond 0.00661 ( 7279) covalent geometry : angle 0.66595 ( 9903) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 121 time to evaluate : 0.740 Fit side-chains REVERT: R 6 THR cc_start: 0.8123 (OUTLIER) cc_final: 0.7843 (p) REVERT: R 59 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7488 (mm-40) REVERT: R 179 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8387 (t) REVERT: R 280 TYR cc_start: 0.8640 (p90) cc_final: 0.8300 (p90) REVERT: R 290 GLN cc_start: 0.8522 (tm-30) cc_final: 0.7870 (tp40) REVERT: R 370 ARG cc_start: 0.7132 (mtm-85) cc_final: 0.5363 (ptt90) REVERT: R 383 MET cc_start: 0.8377 (mtt) cc_final: 0.8097 (mtt) REVERT: A 20 ASP cc_start: 0.7690 (m-30) cc_final: 0.7209 (m-30) REVERT: A 23 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7675 (mt) REVERT: A 205 ARG cc_start: 0.8475 (mmt180) cc_final: 0.8269 (mpt180) REVERT: A 263 SER cc_start: 0.8925 (m) cc_final: 0.8664 (p) REVERT: A 306 GLN cc_start: 0.7590 (tp40) cc_final: 0.7258 (mm-40) REVERT: A 308 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: A 350 ASP cc_start: 0.7645 (m-30) cc_final: 0.7290 (m-30) REVERT: B 52 ARG cc_start: 0.8254 (mtt-85) cc_final: 0.7851 (ptp90) REVERT: B 268 ASN cc_start: 0.8430 (m110) cc_final: 0.7837 (t0) outliers start: 43 outliers final: 20 residues processed: 148 average time/residue: 0.9141 time to fit residues: 144.7418 Evaluate side-chains 138 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 59 GLN Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 386 CYS Chi-restraints excluded: chain R residue 387 CYS Chi-restraints excluded: chain R residue 391 ILE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 73 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** B 142 HIS ** 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 = 0.3721 r_free = 0.3721 target = 0.148248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.111917 restraints weight = 8214.084| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.20 r_work: 0.3153 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 7284 Z= 0.218 Angle : 0.604 9.120 9913 Z= 0.315 Chirality : 0.043 0.212 1166 Planarity : 0.003 0.035 1241 Dihedral : 4.337 25.756 995 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.43 % Allowed : 18.05 % Favored : 76.53 % 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 (0.27), residues: 924 helix: 1.22 (0.27), residues: 382 sheet: -0.73 (0.33), residues: 223 loop : -0.70 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 169 HIS 0.006 0.001 HIS B 142 PHE 0.014 0.002 PHE R 175 TYR 0.018 0.001 TYR B 59 ARG 0.006 0.001 ARG R 328 Details of bonding type rmsd hydrogen bonds : bond 0.04143 ( 383) hydrogen bonds : angle 5.18627 ( 1101) SS BOND : bond 0.00449 ( 5) SS BOND : angle 1.98216 ( 10) covalent geometry : bond 0.00508 ( 7279) covalent geometry : angle 0.60091 ( 9903) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 120 time to evaluate : 0.831 Fit side-chains REVERT: R 6 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.8094 (p) REVERT: R 59 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7445 (mm-40) REVERT: R 280 TYR cc_start: 0.8619 (p90) cc_final: 0.8306 (p90) REVERT: R 290 GLN cc_start: 0.8420 (tm-30) cc_final: 0.7821 (tp40) REVERT: R 370 ARG cc_start: 0.7159 (mtm-85) cc_final: 0.5442 (ptt90) REVERT: R 383 MET cc_start: 0.8248 (mtt) cc_final: 0.7997 (mtt) REVERT: R 384 THR cc_start: 0.8882 (m) cc_final: 0.8635 (t) REVERT: A 20 ASP cc_start: 0.7579 (m-30) cc_final: 0.7082 (m-30) REVERT: A 263 SER cc_start: 0.8901 (m) cc_final: 0.8623 (p) REVERT: A 283 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7387 (tt) REVERT: A 306 GLN cc_start: 0.7535 (tp40) cc_final: 0.7191 (mm-40) REVERT: A 350 ASP cc_start: 0.7667 (m-30) cc_final: 0.7305 (m-30) REVERT: B 52 ARG cc_start: 0.8213 (mtt-85) cc_final: 0.7688 (ptp90) REVERT: B 96 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7830 (ppt-90) REVERT: B 249 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8254 (m) REVERT: B 268 ASN cc_start: 0.8378 (m110) cc_final: 0.7824 (t0) outliers start: 40 outliers final: 15 residues processed: 148 average time/residue: 0.9590 time to fit residues: 151.5038 Evaluate side-chains 133 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 59 GLN Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 386 CYS Chi-restraints excluded: chain R residue 387 CYS Chi-restraints excluded: chain R residue 391 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 58 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 3 optimal weight: 0.4980 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 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 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.153374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.118044 restraints weight = 8118.113| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.10 r_work: 0.3180 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7284 Z= 0.157 Angle : 0.570 8.479 9913 Z= 0.294 Chirality : 0.041 0.192 1166 Planarity : 0.003 0.037 1241 Dihedral : 4.138 25.863 995 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.70 % Allowed : 19.40 % Favored : 74.90 % 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: 0.25 (0.28), residues: 924 helix: 1.43 (0.27), residues: 385 sheet: -0.62 (0.33), residues: 218 loop : -0.69 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 182 HIS 0.004 0.001 HIS B 91 PHE 0.013 0.001 PHE R 205 TYR 0.011 0.001 TYR B 59 ARG 0.008 0.001 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03842 ( 383) hydrogen bonds : angle 5.04266 ( 1101) SS BOND : bond 0.00370 ( 5) SS BOND : angle 1.71273 ( 10) covalent geometry : bond 0.00357 ( 7279) covalent geometry : angle 0.56807 ( 9903) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 121 time to evaluate : 0.796 Fit side-chains REVERT: R 6 THR cc_start: 0.8487 (OUTLIER) cc_final: 0.8133 (p) REVERT: R 280 TYR cc_start: 0.8623 (p90) cc_final: 0.8270 (p90) REVERT: R 290 GLN cc_start: 0.8411 (tm-30) cc_final: 0.7835 (tp40) REVERT: R 291 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8941 (t) REVERT: R 370 ARG cc_start: 0.7256 (mtm-85) cc_final: 0.5552 (ptt90) REVERT: R 384 THR cc_start: 0.8834 (m) cc_final: 0.8590 (t) REVERT: A 20 ASP cc_start: 0.7549 (m-30) cc_final: 0.7098 (m-30) REVERT: A 263 SER cc_start: 0.8853 (m) cc_final: 0.8615 (p) REVERT: A 306 GLN cc_start: 0.7476 (tp40) cc_final: 0.7146 (mm-40) REVERT: A 350 ASP cc_start: 0.7632 (m-30) cc_final: 0.7282 (m-30) REVERT: B 52 ARG cc_start: 0.8185 (mtt-85) cc_final: 0.7677 (ptp90) REVERT: B 249 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.8261 (m) REVERT: B 268 ASN cc_start: 0.8390 (m110) cc_final: 0.7717 (t0) outliers start: 42 outliers final: 18 residues processed: 147 average time/residue: 0.9093 time to fit residues: 143.3294 Evaluate side-chains 135 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 271 HIS Chi-restraints excluded: chain R residue 291 THR Chi-restraints excluded: chain R residue 386 CYS Chi-restraints excluded: chain R residue 387 CYS Chi-restraints excluded: chain R residue 391 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 81 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 86 optimal weight: 0.0470 overall best weight: 1.1080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.149440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.113671 restraints weight = 8182.713| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.17 r_work: 0.3207 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7284 Z= 0.184 Angle : 0.591 8.320 9913 Z= 0.305 Chirality : 0.042 0.193 1166 Planarity : 0.003 0.039 1241 Dihedral : 4.190 25.626 995 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.29 % Allowed : 20.90 % Favored : 73.81 % 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: 0.29 (0.28), residues: 924 helix: 1.62 (0.27), residues: 376 sheet: -0.65 (0.33), residues: 218 loop : -0.78 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 182 HIS 0.009 0.001 HIS B 142 PHE 0.014 0.002 PHE B 292 TYR 0.013 0.001 TYR R 27 ARG 0.014 0.001 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03953 ( 383) hydrogen bonds : angle 5.05919 ( 1101) SS BOND : bond 0.00362 ( 5) SS BOND : angle 1.84543 ( 10) covalent geometry : bond 0.00426 ( 7279) covalent geometry : angle 0.58876 ( 9903) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.821 Fit side-chains REVERT: R 6 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8242 (p) REVERT: R 280 TYR cc_start: 0.8650 (p90) cc_final: 0.8276 (p90) REVERT: R 290 GLN cc_start: 0.8424 (tm-30) cc_final: 0.7845 (tp40) REVERT: R 291 THR cc_start: 0.9267 (OUTLIER) cc_final: 0.8958 (t) REVERT: R 370 ARG cc_start: 0.7318 (mtm-85) cc_final: 0.5653 (ptt90) REVERT: R 384 THR cc_start: 0.8892 (m) cc_final: 0.8666 (t) REVERT: A 20 ASP cc_start: 0.7683 (m-30) cc_final: 0.7191 (m-30) REVERT: A 216 GLU cc_start: 0.8595 (tt0) cc_final: 0.8378 (tt0) REVERT: A 263 SER cc_start: 0.8869 (m) cc_final: 0.8641 (p) REVERT: A 306 GLN cc_start: 0.7537 (tp40) cc_final: 0.7091 (mm-40) REVERT: A 350 ASP cc_start: 0.7678 (m-30) cc_final: 0.7301 (m-30) REVERT: B 52 ARG cc_start: 0.8200 (mtt-85) cc_final: 0.7712 (ptp90) REVERT: B 249 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8319 (m) REVERT: B 268 ASN cc_start: 0.8431 (m110) cc_final: 0.7750 (t0) outliers start: 39 outliers final: 23 residues processed: 145 average time/residue: 0.9827 time to fit residues: 152.0573 Evaluate side-chains 141 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 35 SER Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 291 THR Chi-restraints excluded: chain R residue 386 CYS Chi-restraints excluded: chain R residue 387 CYS Chi-restraints excluded: chain R residue 391 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 0.0970 chunk 84 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.151867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.115864 restraints weight = 8157.855| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.18 r_work: 0.3185 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7284 Z= 0.140 Angle : 0.562 8.124 9913 Z= 0.288 Chirality : 0.041 0.197 1166 Planarity : 0.004 0.073 1241 Dihedral : 4.056 25.815 995 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.21 % Allowed : 22.39 % Favored : 73.41 % 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: 0.43 (0.28), residues: 924 helix: 1.75 (0.27), residues: 376 sheet: -0.61 (0.33), residues: 214 loop : -0.72 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 182 HIS 0.004 0.001 HIS B 142 PHE 0.015 0.001 PHE B 292 TYR 0.013 0.001 TYR R 27 ARG 0.019 0.001 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03743 ( 383) hydrogen bonds : angle 4.95611 ( 1101) SS BOND : bond 0.00308 ( 5) SS BOND : angle 1.50508 ( 10) covalent geometry : bond 0.00318 ( 7279) covalent geometry : angle 0.56015 ( 9903) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.733 Fit side-chains REVERT: R 6 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8236 (p) REVERT: R 280 TYR cc_start: 0.8625 (p90) cc_final: 0.8244 (p90) REVERT: R 290 GLN cc_start: 0.8420 (tm-30) cc_final: 0.7828 (tp40) REVERT: R 291 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.8909 (t) REVERT: R 370 ARG cc_start: 0.7293 (mtm-85) cc_final: 0.5531 (ptt90) REVERT: A 20 ASP cc_start: 0.7597 (m-30) cc_final: 0.7124 (m-30) REVERT: A 263 SER cc_start: 0.8849 (m) cc_final: 0.8601 (p) REVERT: A 306 GLN cc_start: 0.7411 (tp40) cc_final: 0.6971 (mm-40) REVERT: A 308 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: A 350 ASP cc_start: 0.7533 (m-30) cc_final: 0.7176 (m-30) REVERT: B 52 ARG cc_start: 0.8154 (mtt-85) cc_final: 0.7661 (ptp90) REVERT: B 188 MET cc_start: 0.8205 (mmm) cc_final: 0.7937 (mmm) REVERT: B 249 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8310 (m) REVERT: B 268 ASN cc_start: 0.8409 (m110) cc_final: 0.7739 (t0) outliers start: 31 outliers final: 19 residues processed: 144 average time/residue: 0.8587 time to fit residues: 132.6647 Evaluate side-chains 138 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 35 SER Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 291 THR Chi-restraints excluded: chain R residue 386 CYS Chi-restraints excluded: chain R residue 387 CYS Chi-restraints excluded: chain R residue 391 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 56 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 36 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 22 optimal weight: 0.2980 chunk 70 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 0.0570 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 33 GLN ** R 290 GLN ** 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 = 0.3773 r_free = 0.3773 target = 0.153417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.117442 restraints weight = 8184.377| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.20 r_work: 0.3208 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7284 Z= 0.126 Angle : 0.539 7.540 9913 Z= 0.278 Chirality : 0.041 0.184 1166 Planarity : 0.004 0.077 1241 Dihedral : 3.964 25.687 995 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.80 % Allowed : 22.66 % Favored : 73.54 % 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: 0.50 (0.28), residues: 924 helix: 1.80 (0.27), residues: 378 sheet: -0.53 (0.34), residues: 206 loop : -0.72 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 182 HIS 0.004 0.001 HIS B 91 PHE 0.017 0.001 PHE R 181 TYR 0.012 0.001 TYR R 347 ARG 0.019 0.001 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 383) hydrogen bonds : angle 4.86884 ( 1101) SS BOND : bond 0.00249 ( 5) SS BOND : angle 1.40229 ( 10) covalent geometry : bond 0.00284 ( 7279) covalent geometry : angle 0.53700 ( 9903) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.721 Fit side-chains REVERT: R 6 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8223 (p) REVERT: R 280 TYR cc_start: 0.8631 (p90) cc_final: 0.8264 (p90) REVERT: R 290 GLN cc_start: 0.8389 (tm-30) cc_final: 0.7793 (tp40) REVERT: R 291 THR cc_start: 0.9208 (OUTLIER) cc_final: 0.8865 (t) REVERT: R 370 ARG cc_start: 0.7285 (mtm-85) cc_final: 0.5542 (ptt90) REVERT: A 20 ASP cc_start: 0.7589 (m-30) cc_final: 0.7106 (m-30) REVERT: A 263 SER cc_start: 0.8850 (m) cc_final: 0.8574 (p) REVERT: A 306 GLN cc_start: 0.7268 (tp40) cc_final: 0.6852 (mm-40) REVERT: A 350 ASP cc_start: 0.7520 (m-30) cc_final: 0.7155 (m-30) REVERT: B 52 ARG cc_start: 0.8084 (mtt-85) cc_final: 0.7639 (ptp90) REVERT: B 249 THR cc_start: 0.8558 (OUTLIER) cc_final: 0.8249 (m) REVERT: B 268 ASN cc_start: 0.8371 (m110) cc_final: 0.7706 (t0) outliers start: 28 outliers final: 20 residues processed: 139 average time/residue: 0.8984 time to fit residues: 133.6939 Evaluate side-chains 137 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 35 SER Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 291 THR Chi-restraints excluded: chain R residue 386 CYS Chi-restraints excluded: chain R residue 387 CYS Chi-restraints excluded: chain R residue 391 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 79 optimal weight: 0.9980 chunk 57 optimal weight: 30.0000 chunk 44 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 5 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.150468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.113861 restraints weight = 8321.014| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.23 r_work: 0.3183 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7284 Z= 0.183 Angle : 0.586 7.444 9913 Z= 0.304 Chirality : 0.042 0.184 1166 Planarity : 0.004 0.058 1241 Dihedral : 4.073 25.359 995 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.53 % Allowed : 23.47 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.28), residues: 924 helix: 1.78 (0.27), residues: 375 sheet: -0.61 (0.34), residues: 210 loop : -0.71 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 182 HIS 0.007 0.001 HIS B 142 PHE 0.018 0.002 PHE R 181 TYR 0.012 0.001 TYR R 27 ARG 0.014 0.001 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03843 ( 383) hydrogen bonds : angle 4.96042 ( 1101) SS BOND : bond 0.00376 ( 5) SS BOND : angle 1.72129 ( 10) covalent geometry : bond 0.00428 ( 7279) covalent geometry : angle 0.58360 ( 9903) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.752 Fit side-chains REVERT: R 6 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8263 (p) REVERT: R 280 TYR cc_start: 0.8638 (p90) cc_final: 0.8300 (p90) REVERT: R 290 GLN cc_start: 0.8437 (tm-30) cc_final: 0.7840 (tp40) REVERT: R 291 THR cc_start: 0.9250 (OUTLIER) cc_final: 0.8930 (t) REVERT: R 370 ARG cc_start: 0.7325 (mtm-85) cc_final: 0.5599 (ptt90) REVERT: A 20 ASP cc_start: 0.7608 (m-30) cc_final: 0.7103 (m-30) REVERT: A 263 SER cc_start: 0.8847 (m) cc_final: 0.8606 (p) REVERT: A 306 GLN cc_start: 0.7384 (tp40) cc_final: 0.7105 (mm-40) REVERT: A 350 ASP cc_start: 0.7529 (m-30) cc_final: 0.7197 (m-30) REVERT: B 52 ARG cc_start: 0.8065 (mtt-85) cc_final: 0.7631 (ptp90) REVERT: B 249 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8266 (m) REVERT: B 268 ASN cc_start: 0.8366 (m110) cc_final: 0.7711 (t0) outliers start: 26 outliers final: 21 residues processed: 137 average time/residue: 0.9421 time to fit residues: 138.3853 Evaluate side-chains 139 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 35 SER Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 291 THR Chi-restraints excluded: chain R residue 386 CYS Chi-restraints excluded: chain R residue 387 CYS Chi-restraints excluded: chain R residue 391 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 56 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 78 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.152045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.115990 restraints weight = 8151.534| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.19 r_work: 0.3190 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7284 Z= 0.146 Angle : 0.563 7.233 9913 Z= 0.292 Chirality : 0.041 0.186 1166 Planarity : 0.004 0.060 1241 Dihedral : 4.033 25.543 995 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.26 % Allowed : 24.15 % Favored : 72.59 % 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: 0.47 (0.28), residues: 924 helix: 1.80 (0.27), residues: 378 sheet: -0.64 (0.34), residues: 210 loop : -0.69 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP R 182 HIS 0.006 0.001 HIS B 142 PHE 0.020 0.001 PHE R 181 TYR 0.013 0.001 TYR R 27 ARG 0.014 0.001 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03707 ( 383) hydrogen bonds : angle 4.90072 ( 1101) SS BOND : bond 0.00300 ( 5) SS BOND : angle 1.51135 ( 10) covalent geometry : bond 0.00336 ( 7279) covalent geometry : angle 0.56096 ( 9903) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6439.15 seconds wall clock time: 112 minutes 35.09 seconds (6755.09 seconds total)