Starting phenix.real_space_refine on Thu Mar 13 06:53:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f1q_31422/03_2025/7f1q_31422.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f1q_31422/03_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_31422/03_2025/7f1q_31422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f1q_31422/03_2025/7f1q_31422.map" model { file = "/net/cci-nas-00/data/ceres_data/7f1q_31422/03_2025/7f1q_31422.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f1q_31422/03_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-5624/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: 4.83, per 1000 atoms: 0.68 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: 1.82 Conformation dependent library (CDL) restraints added in 1.1 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: 0.76 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: 2.06 Time building geometry restraints manager: 2.15 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: 0.010 Normalize map: mean=0, sd=1: 26.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.550 Find NCS groups from input model: 0.080 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:17.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.740 ------------------------------------------------------------------------------- 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 7279 Z= 0.141 Angle : 0.549 6.692 9903 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 *********************** 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 : 0.765 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: 0.8364 time to fit residues: 154.8644 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 : 0.809 ------------------------------------------------------------------------------- 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: 4.9990 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 7279 Z= 0.465 Angle : 0.701 8.606 9903 Z= 0.370 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 *********************** 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 : 0.779 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: 1.1805 time to fit residues: 197.2422 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 : 0.731 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.155289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.121451 restraints weight = 8230.786| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.03 r_work: 0.3240 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7279 Z= 0.223 Angle : 0.555 9.739 9903 Z= 0.287 Chirality : 0.041 0.211 1166 Planarity : 0.003 0.033 1241 Dihedral : 4.165 25.767 995 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.48 % Allowed : 16.28 % Favored : 79.24 % 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 : -0.73 (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 0.013 0.001 PHE R 175 TYR 0.007 0.001 TYR R 61 ARG 0.005 0.001 ARG R 319 *********************** 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: 33 poor density : 119 time to evaluate : 1.318 Fit side-chains REVERT: R 178 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8909 (t) REVERT: R 290 GLN cc_start: 0.8519 (tm-30) cc_final: 0.7737 (tp40) REVERT: R 334 PHE cc_start: 0.7789 (m-10) cc_final: 0.7471 (m-80) REVERT: R 359 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7815 (t80) REVERT: A 216 GLU cc_start: 0.8599 (tt0) cc_final: 0.8346 (tt0) REVERT: A 308 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: A 350 ASP cc_start: 0.7650 (m-30) cc_final: 0.7294 (m-30) REVERT: B 52 ARG cc_start: 0.8172 (mtt-85) cc_final: 0.7712 (ptp90) REVERT: B 249 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.8010 (m) REVERT: B 268 ASN cc_start: 0.8384 (m110) cc_final: 0.7783 (t0) REVERT: B 280 LYS cc_start: 0.8188 (tptt) cc_final: 0.7946 (tmtm) outliers start: 33 outliers final: 12 residues processed: 138 average time/residue: 0.9121 time to fit residues: 135.4325 Evaluate side-chains 125 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 178 THR 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: 0.9980 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 189 GLN 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.145323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.108837 restraints weight = 8308.272| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.20 r_work: 0.3117 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 7279 Z= 0.519 Angle : 0.697 9.281 9903 Z= 0.366 Chirality : 0.048 0.233 1166 Planarity : 0.004 0.032 1241 Dihedral : 4.595 25.257 995 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 5.56 % Allowed : 17.10 % Favored : 77.34 % 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: -0.17 (0.27), residues: 924 helix: 0.86 (0.26), residues: 383 sheet: -0.75 (0.32), residues: 229 loop : -0.63 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 99 HIS 0.008 0.001 HIS B 142 PHE 0.020 0.002 PHE R 214 TYR 0.010 0.002 TYR B 111 ARG 0.007 0.001 ARG R 328 *********************** 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: 41 poor density : 120 time to evaluate : 0.805 Fit side-chains REVERT: R 6 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7891 (p) REVERT: R 59 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7504 (mm-40) REVERT: R 280 TYR cc_start: 0.8654 (p90) cc_final: 0.8366 (p90) REVERT: R 290 GLN cc_start: 0.8527 (tm-30) cc_final: 0.7866 (tp40) REVERT: R 370 ARG cc_start: 0.7212 (mtm-85) cc_final: 0.5467 (ptt90) REVERT: R 383 MET cc_start: 0.8380 (mtt) cc_final: 0.8090 (mtt) REVERT: A 20 ASP cc_start: 0.7656 (m-30) cc_final: 0.7164 (m-30) REVERT: A 23 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7662 (mt) REVERT: A 205 ARG cc_start: 0.8471 (mmt180) cc_final: 0.8265 (mpt180) REVERT: A 263 SER cc_start: 0.8922 (m) cc_final: 0.8638 (p) REVERT: A 306 GLN cc_start: 0.7527 (tp40) cc_final: 0.7141 (mm-40) REVERT: A 308 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: A 350 ASP cc_start: 0.7636 (m-30) cc_final: 0.7269 (m-30) REVERT: B 52 ARG cc_start: 0.8193 (mtt-85) cc_final: 0.7713 (ptp90) REVERT: B 268 ASN cc_start: 0.8414 (m110) cc_final: 0.7787 (t0) outliers start: 41 outliers final: 23 residues processed: 146 average time/residue: 1.0908 time to fit residues: 169.3443 Evaluate side-chains 141 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 178 THR 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 18 MET Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 190 THR 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: 3.9990 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3747 r_free = 0.3747 target = 0.150641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.114853 restraints weight = 8189.174| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.16 r_work: 0.3170 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7279 Z= 0.241 Angle : 0.560 6.990 9903 Z= 0.293 Chirality : 0.042 0.200 1166 Planarity : 0.003 0.038 1241 Dihedral : 4.282 26.274 995 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.70 % Allowed : 18.05 % Favored : 76.26 % 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: 0.14 (0.27), residues: 924 helix: 1.29 (0.27), residues: 385 sheet: -0.65 (0.33), residues: 218 loop : -0.70 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.004 0.001 HIS B 142 PHE 0.013 0.001 PHE R 205 TYR 0.011 0.001 TYR R 27 ARG 0.006 0.001 ARG R 319 *********************** 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 171 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 0.779 Fit side-chains REVERT: R 6 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.8051 (p) REVERT: R 280 TYR cc_start: 0.8583 (p90) cc_final: 0.8246 (p90) REVERT: R 290 GLN cc_start: 0.8404 (tm-30) cc_final: 0.7795 (tp40) REVERT: R 370 ARG cc_start: 0.7138 (mtm-85) cc_final: 0.5351 (ptt90) REVERT: R 383 MET cc_start: 0.8210 (mtt) cc_final: 0.7944 (mtt) REVERT: R 384 THR cc_start: 0.8820 (m) cc_final: 0.8564 (t) REVERT: A 20 ASP cc_start: 0.7544 (m-30) cc_final: 0.7121 (m-30) REVERT: A 216 GLU cc_start: 0.8597 (tt0) cc_final: 0.8355 (tt0) REVERT: A 263 SER cc_start: 0.8885 (m) cc_final: 0.8624 (p) REVERT: A 306 GLN cc_start: 0.7443 (tp40) cc_final: 0.7107 (mm-40) REVERT: A 350 ASP cc_start: 0.7634 (m-30) cc_final: 0.7263 (m-30) REVERT: B 52 ARG cc_start: 0.8182 (mtt-85) cc_final: 0.7788 (ptp90) REVERT: B 96 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7832 (ppt-90) REVERT: B 101 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8632 (ptm) REVERT: B 249 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8247 (m) REVERT: B 268 ASN cc_start: 0.8367 (m110) cc_final: 0.7805 (t0) outliers start: 42 outliers final: 16 residues processed: 154 average time/residue: 0.9380 time to fit residues: 154.4137 Evaluate side-chains 136 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 173 LEU 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 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 96 ARG 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 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: 6.9990 chunk 85 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 1 optimal weight: 0.0980 chunk 31 optimal weight: 0.0970 chunk 44 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3739 r_free = 0.3739 target = 0.150193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.114417 restraints weight = 8206.063| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.08 r_work: 0.3185 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7279 Z= 0.258 Angle : 0.571 7.621 9903 Z= 0.297 Chirality : 0.042 0.192 1166 Planarity : 0.003 0.037 1241 Dihedral : 4.213 25.904 995 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.02 % Allowed : 20.08 % 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: 0.21 (0.27), residues: 924 helix: 1.43 (0.27), residues: 382 sheet: -0.64 (0.33), residues: 217 loop : -0.75 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 169 HIS 0.004 0.001 HIS B 142 PHE 0.013 0.001 PHE R 205 TYR 0.012 0.001 TYR B 59 ARG 0.013 0.001 ARG B 256 *********************** 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 155 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.748 Fit side-chains REVERT: R 6 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8130 (p) REVERT: R 280 TYR cc_start: 0.8636 (p90) cc_final: 0.8337 (p90) REVERT: R 290 GLN cc_start: 0.8416 (tm-30) cc_final: 0.7830 (tp40) REVERT: R 370 ARG cc_start: 0.7250 (mtm-85) cc_final: 0.5570 (ptt90) REVERT: R 383 MET cc_start: 0.8201 (mtt) cc_final: 0.7828 (mtt) REVERT: R 384 THR cc_start: 0.8839 (m) cc_final: 0.8608 (t) REVERT: A 20 ASP cc_start: 0.7528 (m-30) cc_final: 0.7089 (m-30) REVERT: A 263 SER cc_start: 0.8866 (m) cc_final: 0.8620 (p) REVERT: A 306 GLN cc_start: 0.7475 (tp40) cc_final: 0.7182 (mm-40) REVERT: A 308 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7837 (mp0) REVERT: A 350 ASP cc_start: 0.7693 (m-30) cc_final: 0.7310 (m-30) REVERT: B 52 ARG cc_start: 0.8183 (mtt-85) cc_final: 0.7661 (ptp90) REVERT: B 96 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7829 (ppt-90) REVERT: B 101 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8635 (ptm) REVERT: B 249 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8270 (m) REVERT: B 268 ASN cc_start: 0.8393 (m110) cc_final: 0.7704 (t0) outliers start: 37 outliers final: 21 residues processed: 143 average time/residue: 1.0333 time to fit residues: 157.7792 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 : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 65 LEU 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 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 96 ARG 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 146 LEU 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 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: 3.9990 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.0870 chunk 87 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.9160 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.150482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114448 restraints weight = 8154.712| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.20 r_work: 0.3180 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7279 Z= 0.247 Angle : 0.572 7.331 9903 Z= 0.298 Chirality : 0.042 0.191 1166 Planarity : 0.004 0.073 1241 Dihedral : 4.151 25.867 995 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.88 % Allowed : 20.90 % Favored : 74.22 % 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: 0.33 (0.28), residues: 924 helix: 1.65 (0.27), residues: 376 sheet: -0.66 (0.33), residues: 216 loop : -0.74 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 182 HIS 0.008 0.001 HIS B 142 PHE 0.012 0.001 PHE R 205 TYR 0.013 0.001 TYR R 27 ARG 0.019 0.001 ARG B 256 *********************** 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 152 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 3.304 Fit side-chains REVERT: R 6 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8228 (p) REVERT: R 280 TYR cc_start: 0.8638 (p90) cc_final: 0.8315 (p90) REVERT: R 290 GLN cc_start: 0.8407 (tm-30) cc_final: 0.7801 (tp40) REVERT: R 370 ARG cc_start: 0.7283 (mtm-85) cc_final: 0.5656 (ptt90) REVERT: R 383 MET cc_start: 0.8117 (mtt) cc_final: 0.7806 (mtt) REVERT: R 384 THR cc_start: 0.8848 (m) cc_final: 0.8628 (t) REVERT: A 20 ASP cc_start: 0.7595 (m-30) cc_final: 0.7120 (m-30) REVERT: A 263 SER cc_start: 0.8871 (m) cc_final: 0.8615 (p) REVERT: A 306 GLN cc_start: 0.7459 (tp40) cc_final: 0.7169 (mm-40) REVERT: A 350 ASP cc_start: 0.7659 (m-30) cc_final: 0.7279 (m-30) REVERT: B 52 ARG cc_start: 0.8171 (mtt-85) cc_final: 0.7658 (ptp90) REVERT: B 96 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7862 (ppt-90) REVERT: B 101 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8617 (ptm) REVERT: B 249 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8309 (m) REVERT: B 268 ASN cc_start: 0.8413 (m110) cc_final: 0.7742 (t0) REVERT: B 325 MET cc_start: 0.8038 (tpt) cc_final: 0.7835 (tpp) outliers start: 36 outliers final: 21 residues processed: 142 average time/residue: 1.4586 time to fit residues: 221.2978 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 : 1.244 ------------------------------------------------------------------------------- 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 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 96 ARG 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 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: 0.0980 chunk 84 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 1 optimal weight: 0.2980 chunk 26 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** B 142 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.153028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.117116 restraints weight = 8130.564| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.20 r_work: 0.3197 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7279 Z= 0.191 Angle : 0.547 7.451 9903 Z= 0.282 Chirality : 0.041 0.194 1166 Planarity : 0.004 0.077 1241 Dihedral : 3.999 25.799 995 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.93 % Allowed : 22.25 % 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: 0.42 (0.28), residues: 924 helix: 1.72 (0.27), residues: 379 sheet: -0.63 (0.33), residues: 215 loop : -0.69 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 182 HIS 0.004 0.001 HIS B 142 PHE 0.012 0.001 PHE A 196 TYR 0.014 0.001 TYR R 27 ARG 0.018 0.001 ARG B 256 *********************** 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 154 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.751 Fit side-chains REVERT: R 6 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8205 (p) REVERT: R 280 TYR cc_start: 0.8591 (p90) cc_final: 0.8253 (p90) REVERT: R 290 GLN cc_start: 0.8419 (tm-30) cc_final: 0.7817 (tp40) REVERT: R 291 THR cc_start: 0.9160 (t) cc_final: 0.8907 (m) REVERT: R 370 ARG cc_start: 0.7275 (mtm-85) cc_final: 0.5578 (ptt90) REVERT: R 383 MET cc_start: 0.7971 (mtt) cc_final: 0.7571 (mtt) REVERT: R 384 THR cc_start: 0.8811 (m) cc_final: 0.8588 (t) REVERT: A 20 ASP cc_start: 0.7523 (m-30) cc_final: 0.7042 (m-30) REVERT: A 216 GLU cc_start: 0.8539 (tt0) cc_final: 0.8304 (tt0) REVERT: A 263 SER cc_start: 0.8868 (m) cc_final: 0.8580 (p) REVERT: A 306 GLN cc_start: 0.7346 (tp40) cc_final: 0.6941 (mm-40) REVERT: A 308 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7640 (mp0) REVERT: A 350 ASP cc_start: 0.7530 (m-30) cc_final: 0.7160 (m-30) REVERT: B 52 ARG cc_start: 0.8089 (mtt-85) cc_final: 0.7641 (ptp90) REVERT: B 101 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8536 (ptm) REVERT: B 127 LYS cc_start: 0.7072 (mmtt) cc_final: 0.5840 (pptt) REVERT: B 237 ASN cc_start: 0.7589 (t0) cc_final: 0.7383 (t0) REVERT: B 249 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8283 (m) REVERT: B 268 ASN cc_start: 0.8404 (m110) cc_final: 0.7733 (t0) REVERT: B 322 ASP cc_start: 0.8234 (m-30) cc_final: 0.8029 (m-30) outliers start: 29 outliers final: 19 residues processed: 144 average time/residue: 0.9291 time to fit residues: 143.5202 Evaluate side-chains 142 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 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 101 MET 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 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: 0.1980 chunk 36 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.152623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.116381 restraints weight = 8160.044| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.19 r_work: 0.3270 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7279 Z= 0.209 Angle : 0.549 7.541 9903 Z= 0.284 Chirality : 0.041 0.187 1166 Planarity : 0.004 0.079 1241 Dihedral : 3.997 25.653 995 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.93 % Allowed : 22.52 % 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: 0.42 (0.28), residues: 924 helix: 1.75 (0.27), residues: 378 sheet: -0.64 (0.34), residues: 209 loop : -0.73 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 182 HIS 0.003 0.001 HIS B 91 PHE 0.012 0.001 PHE A 196 TYR 0.014 0.001 TYR R 347 ARG 0.019 0.001 ARG B 256 *********************** 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 147 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.739 Fit side-chains REVERT: R 6 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8238 (p) REVERT: R 280 TYR cc_start: 0.8624 (p90) cc_final: 0.8291 (p90) REVERT: R 290 GLN cc_start: 0.8423 (tm-30) cc_final: 0.7854 (tp40) REVERT: R 291 THR cc_start: 0.9177 (t) cc_final: 0.8942 (m) REVERT: R 370 ARG cc_start: 0.7310 (mtm-85) cc_final: 0.5575 (ptt90) REVERT: R 384 THR cc_start: 0.8850 (m) cc_final: 0.8633 (t) REVERT: A 20 ASP cc_start: 0.7637 (m-30) cc_final: 0.7161 (m-30) REVERT: A 263 SER cc_start: 0.8879 (m) cc_final: 0.8632 (p) REVERT: A 350 ASP cc_start: 0.7532 (m-30) cc_final: 0.7168 (m-30) REVERT: B 52 ARG cc_start: 0.8107 (mtt-85) cc_final: 0.7693 (ptp90) REVERT: B 127 LYS cc_start: 0.7117 (mmtt) cc_final: 0.5904 (pptt) REVERT: B 249 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8302 (m) REVERT: B 268 ASN cc_start: 0.8376 (m110) cc_final: 0.7716 (t0) REVERT: B 322 ASP cc_start: 0.8252 (m-30) cc_final: 0.8050 (m-30) outliers start: 29 outliers final: 22 residues processed: 136 average time/residue: 0.9124 time to fit residues: 133.0503 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 : 0.796 ------------------------------------------------------------------------------- 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 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 161 SER 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: 0.5980 chunk 57 optimal weight: 30.0000 chunk 44 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 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 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 = 0.3764 r_free = 0.3764 target = 0.152570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.116224 restraints weight = 8288.578| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.19 r_work: 0.3189 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7279 Z= 0.223 Angle : 0.561 7.779 9903 Z= 0.289 Chirality : 0.042 0.186 1166 Planarity : 0.004 0.083 1241 Dihedral : 4.017 25.500 995 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.26 % Allowed : 23.47 % 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 (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: 0.42 (0.28), residues: 924 helix: 1.74 (0.27), residues: 378 sheet: -0.68 (0.33), residues: 211 loop : -0.69 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 182 HIS 0.003 0.001 HIS B 91 PHE 0.012 0.001 PHE A 196 TYR 0.012 0.001 TYR R 27 ARG 0.020 0.001 ARG B 256 ********************** 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 141 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.796 Fit side-chains REVERT: R 6 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.8247 (p) REVERT: R 280 TYR cc_start: 0.8599 (p90) cc_final: 0.8248 (p90) REVERT: R 290 GLN cc_start: 0.8428 (tm-30) cc_final: 0.7814 (tp40) REVERT: R 291 THR cc_start: 0.9166 (t) cc_final: 0.8927 (m) REVERT: R 370 ARG cc_start: 0.7350 (mtm-85) cc_final: 0.5574 (ptt90) REVERT: R 384 THR cc_start: 0.8866 (m) cc_final: 0.8640 (t) REVERT: A 20 ASP cc_start: 0.7608 (m-30) cc_final: 0.7136 (m-30) REVERT: A 205 ARG cc_start: 0.8124 (mmt-90) cc_final: 0.7827 (mpt180) REVERT: A 263 SER cc_start: 0.8868 (m) cc_final: 0.8583 (p) REVERT: A 306 GLN cc_start: 0.7337 (tp40) cc_final: 0.6985 (mm-40) REVERT: A 350 ASP cc_start: 0.7524 (m-30) cc_final: 0.7183 (m-30) REVERT: B 52 ARG cc_start: 0.8046 (mtt-85) cc_final: 0.7611 (ptp90) REVERT: B 249 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8272 (m) REVERT: B 268 ASN cc_start: 0.8383 (m110) cc_final: 0.7708 (t0) REVERT: B 322 ASP cc_start: 0.8266 (m-30) cc_final: 0.8045 (m-30) outliers start: 24 outliers final: 20 residues processed: 132 average time/residue: 0.9642 time to fit residues: 136.1855 Evaluate side-chains 138 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 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 161 SER 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: 3.9990 chunk 85 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ** 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 = 0.3749 r_free = 0.3749 target = 0.151360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.115172 restraints weight = 8142.518| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.20 r_work: 0.3219 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7279 Z= 0.249 Angle : 0.576 7.841 9903 Z= 0.298 Chirality : 0.042 0.190 1166 Planarity : 0.004 0.079 1241 Dihedral : 4.070 25.410 995 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.99 % Allowed : 23.88 % Favored : 73.13 % 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: 0.42 (0.28), residues: 924 helix: 1.77 (0.27), residues: 376 sheet: -0.70 (0.33), residues: 211 loop : -0.70 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 182 HIS 0.003 0.001 HIS B 91 PHE 0.012 0.001 PHE R 175 TYR 0.012 0.001 TYR R 27 ARG 0.019 0.001 ARG B 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5959.07 seconds wall clock time: 104 minutes 26.07 seconds (6266.07 seconds total)