Starting phenix.real_space_refine on Tue Mar 3 20:59:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f1q_31422/03_2026/7f1q_31422.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f1q_31422/03_2026/7f1q_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 { model { file = "/net/cci-nas-00/data/ceres_data/7f1q_31422/03_2026/7f1q_31422.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f1q_31422/03_2026/7f1q_31422.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f1q_31422/03_2026/7f1q_31422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f1q_31422/03_2026/7f1q_31422.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ARG:plan': 5, 'GLU:plan': 5, 'ASP:plan': 1, 'PHE:plan': 2, 'ASN:plan1': 2} 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: {'GLU:plan': 8, 'ASP:plan': 7, 'GLN:plan1': 1, 'TYR:plan': 1} 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: {'ARG:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 4, 'GLU:plan': 2, 'TYR:plan': 1} 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: 1.66, per 1000 atoms: 0.23 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: 0.57 Conformation dependent library (CDL) restraints added in 256.6 milliseconds 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: 0.23 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: 1.09 Time building geometry restraints manager: 0.77 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.700 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.340 ------------------------------------------------------------------------------- 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 : 10.28 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.001 0.000 ARG B 52 TYR 0.009 0.001 TYR R 347 PHE 0.008 0.001 PHE A 354 TRP 0.020 0.001 TRP B 169 HIS 0.002 0.000 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 7279) covalent geometry : angle 0.54933 ( 9903) SS BOND : bond 0.00330 ( 5) SS BOND : angle 0.68199 ( 10) hydrogen bonds : bond 0.15087 ( 383) hydrogen bonds : angle 5.96146 ( 1101) *********************** 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 : 0.229 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: 0.4033 time to fit residues: 74.4958 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 : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 R 277 HIS A 255 ASN B 110 ASN B 259 GLN C 44 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.159064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.125321 restraints weight = 8263.181| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.05 r_work: 0.3295 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 7284 Z= 0.243 Angle : 0.631 7.319 9913 Z= 0.333 Chirality : 0.045 0.231 1166 Planarity : 0.004 0.032 1241 Dihedral : 4.095 24.954 995 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.80 % Allowed : 13.16 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.26), residues: 924 helix: 0.66 (0.25), residues: 390 sheet: -0.57 (0.34), residues: 206 loop : -1.09 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 150 TYR 0.016 0.002 TYR B 105 PHE 0.019 0.002 PHE R 285 TRP 0.025 0.002 TRP R 182 HIS 0.006 0.001 HIS R 271 Details of bonding type rmsd covalent geometry : bond 0.00565 ( 7279) covalent geometry : angle 0.62935 ( 9903) SS BOND : bond 0.00315 ( 5) SS BOND : angle 1.60004 ( 10) hydrogen bonds : bond 0.04419 ( 383) hydrogen bonds : angle 4.88511 ( 1101) *********************** 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 163 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.267 Fit side-chains REVERT: R 33 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8383 (mp10) REVERT: R 325 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6634 (mptm) REVERT: R 359 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7914 (t80) REVERT: A 308 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: A 350 ASP cc_start: 0.7614 (m-30) cc_final: 0.7244 (m-30) REVERT: B 52 ARG cc_start: 0.8212 (mtt-85) cc_final: 0.7680 (ptp90) REVERT: B 268 ASN cc_start: 0.8281 (m110) cc_final: 0.7777 (t0) outliers start: 28 outliers final: 12 residues processed: 149 average time/residue: 0.4572 time to fit residues: 72.7478 Evaluate side-chains 132 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 GLN Chi-restraints excluded: chain R residue 135 LEU 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 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 165 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 70 optimal weight: 0.5980 chunk 81 optimal weight: 8.9990 chunk 78 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 184 HIS R 266 GLN R 271 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.159080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.125642 restraints weight = 8250.891| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.01 r_work: 0.3295 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7284 Z= 0.149 Angle : 0.559 9.576 9913 Z= 0.290 Chirality : 0.041 0.195 1166 Planarity : 0.003 0.034 1241 Dihedral : 4.020 26.019 995 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.07 % Allowed : 16.42 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.27), residues: 924 helix: 1.16 (0.26), residues: 393 sheet: -0.45 (0.33), residues: 207 loop : -0.79 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 328 TYR 0.009 0.001 TYR B 111 PHE 0.012 0.001 PHE R 175 TRP 0.019 0.002 TRP R 182 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7279) covalent geometry : angle 0.55648 ( 9903) SS BOND : bond 0.00297 ( 5) SS BOND : angle 1.77677 ( 10) hydrogen bonds : bond 0.03832 ( 383) hydrogen bonds : angle 4.78484 ( 1101) *********************** 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 152 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.278 Fit side-chains REVERT: R 6 THR cc_start: 0.7759 (p) cc_final: 0.7502 (p) REVERT: R 33 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8385 (mp10) REVERT: R 230 VAL cc_start: 0.8633 (m) cc_final: 0.8258 (t) REVERT: R 290 GLN cc_start: 0.8547 (tm-30) cc_final: 0.7741 (tp40) REVERT: R 334 PHE cc_start: 0.7436 (m-10) cc_final: 0.7051 (m-80) REVERT: R 337 MET cc_start: 0.7657 (mmm) cc_final: 0.7353 (mtt) REVERT: R 359 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7847 (t80) REVERT: A 216 GLU cc_start: 0.8385 (tt0) cc_final: 0.8118 (tt0) REVERT: A 308 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: A 350 ASP cc_start: 0.7554 (m-30) cc_final: 0.7175 (m-30) REVERT: B 52 ARG cc_start: 0.8109 (mtt-85) cc_final: 0.7702 (ptp90) REVERT: B 78 LYS cc_start: 0.6774 (mtmt) cc_final: 0.6547 (mppt) REVERT: B 127 LYS cc_start: 0.7206 (mmtt) cc_final: 0.5962 (pptt) REVERT: B 268 ASN cc_start: 0.8370 (m110) cc_final: 0.7809 (t0) outliers start: 30 outliers final: 10 residues processed: 138 average time/residue: 0.4594 time to fit residues: 67.9428 Evaluate side-chains 126 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 GLN 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 81 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 18 GLN R 271 HIS ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.151579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.116709 restraints weight = 8288.335| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.06 r_work: 0.3181 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7284 Z= 0.213 Angle : 0.602 7.911 9913 Z= 0.317 Chirality : 0.043 0.192 1166 Planarity : 0.003 0.030 1241 Dihedral : 4.224 24.793 995 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.43 % Allowed : 16.69 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.27), residues: 924 helix: 1.13 (0.26), residues: 394 sheet: -0.44 (0.35), residues: 209 loop : -0.71 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 328 TYR 0.011 0.001 TYR B 124 PHE 0.014 0.002 PHE R 214 TRP 0.015 0.002 TRP R 182 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 7279) covalent geometry : angle 0.59835 ( 9903) SS BOND : bond 0.00384 ( 5) SS BOND : angle 2.29729 ( 10) hydrogen bonds : bond 0.04057 ( 383) hydrogen bonds : angle 4.96275 ( 1101) *********************** 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 161 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.268 Fit side-chains REVERT: R 6 THR cc_start: 0.7974 (p) cc_final: 0.7726 (p) REVERT: R 65 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7507 (mm) REVERT: R 151 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7874 (mp) REVERT: R 179 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.8346 (t) REVERT: R 290 GLN cc_start: 0.8520 (tm-30) cc_final: 0.7810 (tp40) REVERT: R 291 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8911 (t) REVERT: R 370 ARG cc_start: 0.6875 (mtm-85) cc_final: 0.4826 (ptt90) REVERT: A 20 ASP cc_start: 0.7568 (m-30) cc_final: 0.7151 (m-30) REVERT: A 205 ARG cc_start: 0.8438 (mmt180) cc_final: 0.8226 (mpt180) REVERT: A 216 GLU cc_start: 0.8625 (tt0) cc_final: 0.8364 (tt0) REVERT: A 263 SER cc_start: 0.8870 (m) cc_final: 0.8623 (p) REVERT: A 306 GLN cc_start: 0.7231 (tp40) cc_final: 0.6889 (mm-40) REVERT: A 308 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: A 350 ASP cc_start: 0.7666 (m-30) cc_final: 0.7311 (m-30) REVERT: B 52 ARG cc_start: 0.8196 (mtt-85) cc_final: 0.7770 (ptp90) REVERT: B 101 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8800 (ptm) REVERT: B 127 LYS cc_start: 0.7165 (mmtt) cc_final: 0.6021 (pptt) REVERT: B 268 ASN cc_start: 0.8444 (m110) cc_final: 0.7802 (t0) outliers start: 40 outliers final: 16 residues processed: 147 average time/residue: 0.4409 time to fit residues: 69.4940 Evaluate side-chains 131 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 136 VAL 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 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 B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 201 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 5 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 1 optimal weight: 0.0030 chunk 26 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 33 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 = 0.3791 r_free = 0.3791 target = 0.154246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.117972 restraints weight = 8163.249| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.14 r_work: 0.3258 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7284 Z= 0.143 Angle : 0.540 6.750 9913 Z= 0.281 Chirality : 0.041 0.189 1166 Planarity : 0.003 0.034 1241 Dihedral : 4.022 25.362 995 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.16 % Allowed : 17.77 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.28), residues: 924 helix: 1.43 (0.26), residues: 387 sheet: -0.52 (0.35), residues: 210 loop : -0.62 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 328 TYR 0.014 0.001 TYR R 61 PHE 0.013 0.001 PHE R 175 TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 7279) covalent geometry : angle 0.53758 ( 9903) SS BOND : bond 0.00307 ( 5) SS BOND : angle 1.59904 ( 10) hydrogen bonds : bond 0.03660 ( 383) hydrogen bonds : angle 4.83138 ( 1101) *********************** 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 158 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 0.351 Fit side-chains REVERT: R 6 THR cc_start: 0.7901 (p) cc_final: 0.7635 (p) REVERT: R 290 GLN cc_start: 0.8430 (tm-30) cc_final: 0.7836 (tp40) REVERT: R 291 THR cc_start: 0.9205 (OUTLIER) cc_final: 0.8880 (t) REVERT: R 359 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7770 (t80) REVERT: R 370 ARG cc_start: 0.6925 (mtm-85) cc_final: 0.4978 (ptt90) REVERT: A 20 ASP cc_start: 0.7518 (m-30) cc_final: 0.7101 (m-30) REVERT: A 216 GLU cc_start: 0.8532 (tt0) cc_final: 0.8273 (tt0) REVERT: A 263 SER cc_start: 0.8880 (m) cc_final: 0.8631 (p) REVERT: A 306 GLN cc_start: 0.7255 (tp40) cc_final: 0.6883 (mm-40) REVERT: A 308 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: A 350 ASP cc_start: 0.7639 (m-30) cc_final: 0.7241 (m-30) REVERT: B 52 ARG cc_start: 0.8084 (mtt-85) cc_final: 0.7738 (ptp90) REVERT: B 101 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8638 (ptm) REVERT: B 127 LYS cc_start: 0.7265 (mmtt) cc_final: 0.5967 (pptt) REVERT: B 188 MET cc_start: 0.8133 (mmm) cc_final: 0.7910 (mmm) REVERT: B 249 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8161 (m) REVERT: B 268 ASN cc_start: 0.8448 (m110) cc_final: 0.7784 (t0) outliers start: 38 outliers final: 18 residues processed: 146 average time/residue: 0.4062 time to fit residues: 63.6559 Evaluate side-chains 134 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 152 ILE 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 359 PHE Chi-restraints excluded: chain R residue 384 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 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 101 MET Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 201 SER 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 52 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 85 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 271 HIS B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.153078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.117497 restraints weight = 8165.689| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.17 r_work: 0.3218 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7284 Z= 0.150 Angle : 0.540 7.179 9913 Z= 0.282 Chirality : 0.041 0.188 1166 Planarity : 0.003 0.036 1241 Dihedral : 3.992 25.004 995 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.21 % Allowed : 19.40 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.28), residues: 924 helix: 1.56 (0.26), residues: 387 sheet: -0.56 (0.35), residues: 207 loop : -0.60 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 319 TYR 0.012 0.001 TYR B 124 PHE 0.015 0.001 PHE R 175 TRP 0.012 0.001 TRP R 182 HIS 0.008 0.001 HIS R 271 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7279) covalent geometry : angle 0.53768 ( 9903) SS BOND : bond 0.00399 ( 5) SS BOND : angle 1.78666 ( 10) hydrogen bonds : bond 0.03687 ( 383) hydrogen bonds : angle 4.82031 ( 1101) *********************** 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 148 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.214 Fit side-chains REVERT: R 6 THR cc_start: 0.7992 (p) cc_final: 0.7703 (p) REVERT: R 290 GLN cc_start: 0.8446 (tm-30) cc_final: 0.7843 (tp40) REVERT: R 291 THR cc_start: 0.9191 (t) cc_final: 0.8860 (t) REVERT: R 370 ARG cc_start: 0.6999 (mtm-85) cc_final: 0.5191 (ptt90) REVERT: A 20 ASP cc_start: 0.7538 (m-30) cc_final: 0.7093 (m-30) REVERT: A 216 GLU cc_start: 0.8551 (tt0) cc_final: 0.8301 (tt0) REVERT: A 263 SER cc_start: 0.8900 (m) cc_final: 0.8643 (p) REVERT: A 306 GLN cc_start: 0.7270 (tp40) cc_final: 0.6906 (mm-40) REVERT: A 308 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: A 350 ASP cc_start: 0.7669 (m-30) cc_final: 0.7296 (m-30) REVERT: B 52 ARG cc_start: 0.8103 (mtt-85) cc_final: 0.7751 (ptp90) REVERT: B 78 LYS cc_start: 0.7176 (mppt) cc_final: 0.6949 (mppt) REVERT: B 101 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8673 (ptm) REVERT: B 127 LYS cc_start: 0.7228 (mmtt) cc_final: 0.5918 (pptt) REVERT: B 268 ASN cc_start: 0.8372 (m110) cc_final: 0.7803 (t0) outliers start: 31 outliers final: 19 residues processed: 138 average time/residue: 0.4496 time to fit residues: 66.3205 Evaluate side-chains 130 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 152 ILE 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 384 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 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 101 MET Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 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 56 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.151643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.115931 restraints weight = 8181.313| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.13 r_work: 0.3191 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7284 Z= 0.165 Angle : 0.551 7.020 9913 Z= 0.287 Chirality : 0.042 0.198 1166 Planarity : 0.003 0.036 1241 Dihedral : 4.018 24.649 995 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.34 % Allowed : 20.08 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.28), residues: 924 helix: 1.67 (0.27), residues: 378 sheet: -0.57 (0.33), residues: 225 loop : -0.54 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 319 TYR 0.012 0.001 TYR B 124 PHE 0.014 0.001 PHE R 175 TRP 0.014 0.002 TRP R 182 HIS 0.008 0.001 HIS R 271 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 7279) covalent geometry : angle 0.54792 ( 9903) SS BOND : bond 0.00323 ( 5) SS BOND : angle 1.79575 ( 10) hydrogen bonds : bond 0.03776 ( 383) hydrogen bonds : angle 4.84585 ( 1101) *********************** 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 148 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.244 Fit side-chains REVERT: R 6 THR cc_start: 0.8099 (p) cc_final: 0.7888 (p) REVERT: R 280 TYR cc_start: 0.8660 (p90) cc_final: 0.8304 (p90) REVERT: R 290 GLN cc_start: 0.8447 (tm-30) cc_final: 0.7869 (tp40) REVERT: R 370 ARG cc_start: 0.7214 (mtm-85) cc_final: 0.5465 (ptt90) REVERT: A 20 ASP cc_start: 0.7591 (m-30) cc_final: 0.7118 (m-30) REVERT: A 216 GLU cc_start: 0.8536 (tt0) cc_final: 0.8275 (tt0) REVERT: A 263 SER cc_start: 0.8875 (m) cc_final: 0.8602 (p) REVERT: A 306 GLN cc_start: 0.7352 (tp40) cc_final: 0.6960 (mm-40) REVERT: A 350 ASP cc_start: 0.7671 (m-30) cc_final: 0.7302 (m-30) REVERT: B 52 ARG cc_start: 0.8100 (mtt-85) cc_final: 0.7750 (ptp90) REVERT: B 78 LYS cc_start: 0.7275 (mppt) cc_final: 0.7065 (mppt) REVERT: B 101 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8732 (ptm) REVERT: B 188 MET cc_start: 0.8170 (mmm) cc_final: 0.7922 (mmm) REVERT: B 268 ASN cc_start: 0.8433 (m110) cc_final: 0.7800 (t0) outliers start: 32 outliers final: 22 residues processed: 137 average time/residue: 0.4583 time to fit residues: 67.0804 Evaluate side-chains 135 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 152 ILE 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 257 LEU Chi-restraints excluded: chain R residue 271 HIS Chi-restraints excluded: chain R residue 375 MET 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 79 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 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 18 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3753 r_free = 0.3753 target = 0.151294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.115458 restraints weight = 8212.719| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.13 r_work: 0.3183 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7284 Z= 0.175 Angle : 0.566 7.112 9913 Z= 0.295 Chirality : 0.042 0.196 1166 Planarity : 0.003 0.037 1241 Dihedral : 4.061 24.822 995 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.80 % Allowed : 21.17 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.28), residues: 924 helix: 1.55 (0.26), residues: 385 sheet: -0.54 (0.33), residues: 219 loop : -0.56 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 319 TYR 0.010 0.001 TYR R 27 PHE 0.013 0.001 PHE R 175 TRP 0.018 0.002 TRP R 182 HIS 0.015 0.001 HIS R 271 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 7279) covalent geometry : angle 0.56288 ( 9903) SS BOND : bond 0.00376 ( 5) SS BOND : angle 1.81353 ( 10) hydrogen bonds : bond 0.03831 ( 383) hydrogen bonds : angle 4.89737 ( 1101) *********************** 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 141 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.213 Fit side-chains REVERT: R 6 THR cc_start: 0.8476 (p) cc_final: 0.8217 (p) REVERT: R 280 TYR cc_start: 0.8650 (p90) cc_final: 0.8290 (p90) REVERT: R 290 GLN cc_start: 0.8454 (tm-30) cc_final: 0.7879 (tp40) REVERT: R 370 ARG cc_start: 0.7234 (mtm-85) cc_final: 0.5492 (ptt90) REVERT: A 20 ASP cc_start: 0.7577 (m-30) cc_final: 0.7074 (m-30) REVERT: A 263 SER cc_start: 0.8861 (m) cc_final: 0.8625 (p) REVERT: A 306 GLN cc_start: 0.7441 (tp40) cc_final: 0.7034 (mm-40) REVERT: A 308 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7679 (mp0) REVERT: A 350 ASP cc_start: 0.7670 (m-30) cc_final: 0.7301 (m-30) REVERT: B 52 ARG cc_start: 0.8098 (mtt-85) cc_final: 0.7753 (ptp90) REVERT: B 268 ASN cc_start: 0.8369 (m110) cc_final: 0.7795 (t0) outliers start: 28 outliers final: 23 residues processed: 132 average time/residue: 0.4744 time to fit residues: 66.7539 Evaluate side-chains 133 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 152 ILE 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 257 LEU 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 79 LEU 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 201 SER 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 262 MET 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 65 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 0.0050 chunk 16 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.152784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.117580 restraints weight = 8116.653| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.07 r_work: 0.3214 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7284 Z= 0.141 Angle : 0.547 6.831 9913 Z= 0.284 Chirality : 0.041 0.187 1166 Planarity : 0.003 0.037 1241 Dihedral : 3.982 25.071 995 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.39 % Allowed : 21.85 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.28), residues: 924 helix: 1.70 (0.27), residues: 380 sheet: -0.51 (0.33), residues: 219 loop : -0.59 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 256 TYR 0.010 0.001 TYR R 27 PHE 0.017 0.001 PHE R 181 TRP 0.018 0.002 TRP R 182 HIS 0.010 0.001 HIS R 271 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 7279) covalent geometry : angle 0.54550 ( 9903) SS BOND : bond 0.00397 ( 5) SS BOND : angle 1.55307 ( 10) hydrogen bonds : bond 0.03655 ( 383) hydrogen bonds : angle 4.82938 ( 1101) *********************** 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 143 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.265 Fit side-chains REVERT: R 6 THR cc_start: 0.8536 (p) cc_final: 0.8288 (p) REVERT: R 280 TYR cc_start: 0.8655 (p90) cc_final: 0.8292 (p90) REVERT: R 290 GLN cc_start: 0.8433 (tm-30) cc_final: 0.7873 (tp40) REVERT: R 370 ARG cc_start: 0.7220 (mtm-85) cc_final: 0.5477 (ptt90) REVERT: A 20 ASP cc_start: 0.7575 (m-30) cc_final: 0.7084 (m-30) REVERT: A 205 ARG cc_start: 0.8068 (mmt-90) cc_final: 0.7684 (mpt180) REVERT: A 263 SER cc_start: 0.8870 (m) cc_final: 0.8599 (p) REVERT: A 306 GLN cc_start: 0.7391 (tp40) cc_final: 0.7017 (mm-40) REVERT: A 350 ASP cc_start: 0.7674 (m-30) cc_final: 0.7290 (m-30) REVERT: B 52 ARG cc_start: 0.8084 (mtt-85) cc_final: 0.7746 (ptp90) REVERT: B 188 MET cc_start: 0.8140 (mmm) cc_final: 0.7899 (mmm) REVERT: B 237 ASN cc_start: 0.7600 (t0) cc_final: 0.7393 (t0) REVERT: B 268 ASN cc_start: 0.8380 (m110) cc_final: 0.7797 (t0) outliers start: 25 outliers final: 22 residues processed: 136 average time/residue: 0.4721 time to fit residues: 68.4420 Evaluate side-chains 134 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 152 ILE 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 257 LEU 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 79 LEU 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 201 SER 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 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 20 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 80 optimal weight: 0.0270 chunk 53 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 194 ASN ** R 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3786 r_free = 0.3786 target = 0.154400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.119210 restraints weight = 8144.674| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.13 r_work: 0.3231 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7284 Z= 0.125 Angle : 0.551 8.606 9913 Z= 0.284 Chirality : 0.041 0.183 1166 Planarity : 0.004 0.066 1241 Dihedral : 3.944 25.068 995 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.26 % Allowed : 22.80 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.28), residues: 924 helix: 1.79 (0.27), residues: 380 sheet: -0.46 (0.33), residues: 212 loop : -0.65 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 256 TYR 0.010 0.001 TYR R 27 PHE 0.018 0.001 PHE R 181 TRP 0.023 0.002 TRP R 182 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7279) covalent geometry : angle 0.54945 ( 9903) SS BOND : bond 0.00296 ( 5) SS BOND : angle 1.38715 ( 10) hydrogen bonds : bond 0.03536 ( 383) hydrogen bonds : angle 4.74237 ( 1101) ********************** 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 140 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.282 Fit side-chains REVERT: R 6 THR cc_start: 0.8547 (p) cc_final: 0.8299 (p) REVERT: R 280 TYR cc_start: 0.8643 (p90) cc_final: 0.8276 (p90) REVERT: R 290 GLN cc_start: 0.8412 (tm-30) cc_final: 0.7840 (tp40) REVERT: R 291 THR cc_start: 0.9173 (t) cc_final: 0.8757 (m) REVERT: R 370 ARG cc_start: 0.7218 (mtm-85) cc_final: 0.5474 (ptt90) REVERT: A 20 ASP cc_start: 0.7576 (m-30) cc_final: 0.7087 (m-30) REVERT: A 205 ARG cc_start: 0.8124 (mmt-90) cc_final: 0.7755 (mpt180) REVERT: A 263 SER cc_start: 0.8869 (m) cc_final: 0.8616 (p) REVERT: A 350 ASP cc_start: 0.7673 (m-30) cc_final: 0.7292 (m-30) REVERT: B 52 ARG cc_start: 0.8035 (mtt-85) cc_final: 0.7732 (ptp90) REVERT: B 188 MET cc_start: 0.8043 (mmm) cc_final: 0.7817 (mmm) REVERT: B 268 ASN cc_start: 0.8374 (m110) cc_final: 0.7782 (t0) outliers start: 24 outliers final: 21 residues processed: 133 average time/residue: 0.5051 time to fit residues: 71.4724 Evaluate side-chains 131 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 TYR Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 152 ILE 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 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 79 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 201 SER 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 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 25 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 66 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3771 r_free = 0.3771 target = 0.152904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.117719 restraints weight = 8133.525| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.08 r_work: 0.3244 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7284 Z= 0.148 Angle : 0.572 7.755 9913 Z= 0.296 Chirality : 0.042 0.181 1166 Planarity : 0.004 0.086 1241 Dihedral : 3.982 24.970 995 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.99 % Allowed : 23.74 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.28), residues: 924 helix: 1.81 (0.27), residues: 380 sheet: -0.41 (0.33), residues: 213 loop : -0.65 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 256 TYR 0.010 0.001 TYR R 27 PHE 0.020 0.001 PHE R 181 TRP 0.027 0.002 TRP R 182 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 7279) covalent geometry : angle 0.57034 ( 9903) SS BOND : bond 0.00308 ( 5) SS BOND : angle 1.52104 ( 10) hydrogen bonds : bond 0.03676 ( 383) hydrogen bonds : angle 4.78712 ( 1101) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2908.35 seconds wall clock time: 50 minutes 15.11 seconds (3015.11 seconds total)