Starting phenix.real_space_refine on Thu Feb 13 05:06:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f1q_31422/02_2025/7f1q_31422.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f1q_31422/02_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_31422/02_2025/7f1q_31422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f1q_31422/02_2025/7f1q_31422.map" model { file = "/net/cci-nas-00/data/ceres_data/7f1q_31422/02_2025/7f1q_31422.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f1q_31422/02_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-5592/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: 4.43, per 1000 atoms: 0.62 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: 1.70 Conformation dependent library (CDL) restraints added in 989.4 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: 0.74 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: 2.12 Time building geometry restraints manager: 2.00 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.750 Find NCS groups from input model: 0.090 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:14.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.450 ------------------------------------------------------------------------------- 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 : 0.770 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: 0.8833 time to fit residues: 163.5169 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 : 0.799 ------------------------------------------------------------------------------- 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 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.152279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.117259 restraints weight = 8246.287| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.08 r_work: 0.3199 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 7279 Z= 0.466 Angle : 0.708 8.362 9903 Z= 0.374 Chirality : 0.048 0.225 1166 Planarity : 0.004 0.033 1241 Dihedral : 4.565 24.196 995 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % 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: -0.49 (0.26), residues: 924 helix: 0.45 (0.25), residues: 386 sheet: -0.53 (0.34), residues: 208 loop : -0.94 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP R 182 HIS 0.007 0.002 HIS R 271 PHE 0.025 0.003 PHE R 285 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 171 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.738 Fit side-chains REVERT: R 280 TYR cc_start: 0.8625 (p90) cc_final: 0.8263 (p90) REVERT: R 290 GLN cc_start: 0.8535 (tm-30) cc_final: 0.7573 (tp40) REVERT: R 325 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.6934 (mptm) REVERT: R 359 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7926 (t80) REVERT: A 20 ASP cc_start: 0.7555 (m-30) cc_final: 0.7228 (m-30) REVERT: A 216 GLU cc_start: 0.8688 (tt0) cc_final: 0.8457 (tt0) REVERT: A 306 GLN cc_start: 0.7198 (tp40) cc_final: 0.6863 (mm-40) REVERT: A 308 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: A 350 ASP cc_start: 0.7611 (m-30) cc_final: 0.7256 (m-30) REVERT: B 52 ARG cc_start: 0.8218 (mtt-85) cc_final: 0.7816 (ptp90) REVERT: B 268 ASN cc_start: 0.8282 (m110) cc_final: 0.7826 (t0) REVERT: B 280 LYS cc_start: 0.8217 (tptt) cc_final: 0.8006 (tmtm) outliers start: 33 outliers final: 17 residues processed: 155 average time/residue: 1.0275 time to fit residues: 170.3022 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 : 0.847 ------------------------------------------------------------------------------- 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: 0.9990 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 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 = 0.3808 r_free = 0.3808 target = 0.155641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.120428 restraints weight = 8201.231| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.11 r_work: 0.3265 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7279 Z= 0.215 Angle : 0.549 9.712 9903 Z= 0.284 Chirality : 0.041 0.211 1166 Planarity : 0.003 0.033 1241 Dihedral : 4.148 26.022 995 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.61 % Allowed : 16.55 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.27), residues: 924 helix: 1.01 (0.26), residues: 392 sheet: -0.45 (0.35), residues: 200 loop : -0.79 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 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 0.006 0.001 ARG R 328 *********************** 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 156 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 0.774 Fit side-chains REVERT: R 230 VAL cc_start: 0.8718 (m) cc_final: 0.8361 (t) REVERT: R 290 GLN cc_start: 0.8536 (tm-30) cc_final: 0.7787 (tp40) REVERT: R 334 PHE cc_start: 0.7942 (m-10) cc_final: 0.7654 (m-80) REVERT: R 359 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7849 (t80) REVERT: R 383 MET cc_start: 0.8158 (mtt) cc_final: 0.7786 (mtt) REVERT: A 20 ASP cc_start: 0.7522 (m-30) cc_final: 0.7161 (m-30) REVERT: A 216 GLU cc_start: 0.8608 (tt0) cc_final: 0.8365 (tt0) REVERT: A 308 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7785 (mp0) REVERT: A 350 ASP cc_start: 0.7616 (m-30) cc_final: 0.7271 (m-30) REVERT: B 52 ARG cc_start: 0.8205 (mtt-85) cc_final: 0.7777 (ptp90) REVERT: B 188 MET cc_start: 0.8185 (mmm) cc_final: 0.7894 (mmm) REVERT: B 249 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.8050 (m) REVERT: B 268 ASN cc_start: 0.8351 (m110) cc_final: 0.7747 (t0) REVERT: B 280 LYS cc_start: 0.8254 (tptt) cc_final: 0.7996 (tmtm) outliers start: 34 outliers final: 12 residues processed: 143 average time/residue: 0.9070 time to fit residues: 139.3168 Evaluate side-chains 126 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 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 105 TYR 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: 0.0970 chunk 86 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- 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 ** 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 = 0.3741 r_free = 0.3741 target = 0.149773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.113477 restraints weight = 8262.019| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.19 r_work: 0.3166 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 7279 Z= 0.364 Angle : 0.612 8.199 9903 Z= 0.321 Chirality : 0.044 0.214 1166 Planarity : 0.003 0.031 1241 Dihedral : 4.275 25.392 995 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 5.29 % Allowed : 16.96 % Favored : 77.75 % 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: 0.08 (0.27), residues: 924 helix: 1.15 (0.26), residues: 386 sheet: -0.65 (0.33), residues: 223 loop : -0.63 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 182 HIS 0.006 0.001 HIS B 142 PHE 0.014 0.002 PHE R 214 TYR 0.011 0.001 TYR R 61 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 156 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.829 Fit side-chains REVERT: R 120 ASN cc_start: 0.7664 (m110) cc_final: 0.7453 (m-40) REVERT: R 280 TYR cc_start: 0.8610 (p90) cc_final: 0.8259 (p90) REVERT: R 290 GLN cc_start: 0.8509 (tm-30) cc_final: 0.7826 (tp40) REVERT: R 370 ARG cc_start: 0.7042 (mtm-85) cc_final: 0.5115 (ptt90) REVERT: R 383 MET cc_start: 0.8276 (mtt) cc_final: 0.8058 (mtt) REVERT: R 384 THR cc_start: 0.8949 (m) cc_final: 0.8692 (t) REVERT: A 20 ASP cc_start: 0.7568 (m-30) cc_final: 0.7147 (m-30) REVERT: A 23 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7582 (mt) REVERT: A 205 ARG cc_start: 0.8435 (mmt180) cc_final: 0.8234 (mpt180) REVERT: A 306 GLN cc_start: 0.7365 (tp40) cc_final: 0.7088 (mm-40) REVERT: A 308 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: A 350 ASP cc_start: 0.7653 (m-30) cc_final: 0.7295 (m-30) REVERT: B 52 ARG cc_start: 0.8224 (mtt-85) cc_final: 0.7789 (ptp90) REVERT: B 249 THR cc_start: 0.8466 (OUTLIER) cc_final: 0.8144 (m) REVERT: B 268 ASN cc_start: 0.8452 (m110) cc_final: 0.7868 (t0) outliers start: 39 outliers final: 17 residues processed: 141 average time/residue: 1.0238 time to fit residues: 154.1456 Evaluate side-chains 132 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 136 VAL Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 386 CYS Chi-restraints excluded: chain R residue 387 CYS Chi-restraints excluded: chain R residue 391 ILE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 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 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: 7.9990 chunk 6 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 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 = 0.3770 r_free = 0.3770 target = 0.152462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.117941 restraints weight = 8157.602| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.03 r_work: 0.3224 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4292 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= 0.227 Angle : 0.543 6.824 9903 Z= 0.284 Chirality : 0.041 0.190 1166 Planarity : 0.003 0.037 1241 Dihedral : 4.093 25.574 995 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.88 % Allowed : 17.91 % Favored : 77.20 % 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: 0.23 (0.28), residues: 924 helix: 1.35 (0.27), residues: 391 sheet: -0.70 (0.33), residues: 220 loop : -0.60 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS B 142 PHE 0.012 0.001 PHE R 205 TYR 0.013 0.001 TYR B 59 ARG 0.008 0.001 ARG B 256 *********************** 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 161 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.774 Fit side-chains REVERT: R 6 THR cc_start: 0.7789 (OUTLIER) cc_final: 0.7473 (p) REVERT: R 120 ASN cc_start: 0.7660 (m110) cc_final: 0.7450 (m-40) REVERT: R 280 TYR cc_start: 0.8611 (p90) cc_final: 0.8275 (p90) REVERT: R 290 GLN cc_start: 0.8473 (tm-30) cc_final: 0.7890 (tp40) REVERT: R 291 THR cc_start: 0.9193 (t) cc_final: 0.8971 (t) REVERT: R 370 ARG cc_start: 0.7081 (mtm-85) cc_final: 0.5297 (ptt90) REVERT: R 384 THR cc_start: 0.8902 (m) cc_final: 0.8651 (t) REVERT: A 20 ASP cc_start: 0.7586 (m-30) cc_final: 0.7190 (m-30) REVERT: A 205 ARG cc_start: 0.8368 (mmt180) cc_final: 0.8160 (mpt180) REVERT: A 216 GLU cc_start: 0.8637 (tt0) cc_final: 0.8395 (tt0) REVERT: A 306 GLN cc_start: 0.7354 (tp40) cc_final: 0.6936 (mm-40) REVERT: A 308 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: A 350 ASP cc_start: 0.7656 (m-30) cc_final: 0.7269 (m-30) REVERT: B 52 ARG cc_start: 0.8188 (mtt-85) cc_final: 0.7813 (ptp90) REVERT: B 101 MET cc_start: 0.8848 (ptp) cc_final: 0.8612 (ptm) REVERT: B 249 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8209 (m) REVERT: B 268 ASN cc_start: 0.8437 (m110) cc_final: 0.7836 (t0) outliers start: 36 outliers final: 15 residues processed: 145 average time/residue: 0.9316 time to fit residues: 144.9124 Evaluate side-chains 132 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 179 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 386 CYS Chi-restraints excluded: chain R residue 387 CYS Chi-restraints excluded: chain R residue 391 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 316 THR 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 Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 58 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.145387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.109105 restraints weight = 8282.259| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.08 r_work: 0.3106 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 7279 Z= 0.476 Angle : 0.681 9.357 9903 Z= 0.355 Chirality : 0.047 0.221 1166 Planarity : 0.004 0.034 1241 Dihedral : 4.574 24.851 995 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 6.24 % Allowed : 17.77 % Favored : 75.98 % 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: -0.04 (0.27), residues: 924 helix: 1.12 (0.26), residues: 382 sheet: -0.84 (0.32), residues: 228 loop : -0.66 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.009 0.001 HIS B 142 PHE 0.018 0.002 PHE R 214 TYR 0.012 0.002 TYR R 347 ARG 0.014 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 164 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 118 time to evaluate : 0.793 Fit side-chains REVERT: R 6 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.8088 (p) REVERT: R 120 ASN cc_start: 0.7748 (m110) cc_final: 0.7527 (m-40) REVERT: R 178 THR cc_start: 0.9176 (t) cc_final: 0.8969 (t) REVERT: R 280 TYR cc_start: 0.8632 (p90) cc_final: 0.8335 (p90) REVERT: R 290 GLN cc_start: 0.8471 (tm-30) cc_final: 0.7854 (tp40) REVERT: R 337 MET cc_start: 0.8322 (mtt) cc_final: 0.8057 (mtm) REVERT: R 370 ARG cc_start: 0.7328 (mtm-85) cc_final: 0.5708 (ptt90) REVERT: A 20 ASP cc_start: 0.7699 (m-30) cc_final: 0.7169 (m-30) REVERT: A 205 ARG cc_start: 0.8451 (mmt180) cc_final: 0.8240 (mpt180) REVERT: A 263 SER cc_start: 0.8909 (m) cc_final: 0.8620 (p) REVERT: A 306 GLN cc_start: 0.7529 (tp40) cc_final: 0.7182 (mm-40) REVERT: A 350 ASP cc_start: 0.7546 (m-30) cc_final: 0.7205 (m-30) REVERT: B 52 ARG cc_start: 0.8225 (mtt-85) cc_final: 0.7711 (ptp90) REVERT: B 268 ASN cc_start: 0.8367 (m110) cc_final: 0.7777 (t0) outliers start: 46 outliers final: 25 residues processed: 148 average time/residue: 0.9543 time to fit residues: 151.3681 Evaluate side-chains 140 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 113 SER 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 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 198 MET 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 105 TYR 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 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: 1.9990 chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 chunk 87 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.151488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.114669 restraints weight = 8130.170| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.14 r_work: 0.3210 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7279 Z= 0.223 Angle : 0.565 7.055 9903 Z= 0.294 Chirality : 0.041 0.200 1166 Planarity : 0.004 0.069 1241 Dihedral : 4.224 25.979 995 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.61 % Allowed : 20.90 % Favored : 74.49 % 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: 0.23 (0.28), residues: 924 helix: 1.48 (0.27), residues: 381 sheet: -0.69 (0.33), residues: 218 loop : -0.71 (0.34), residues: 325 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 205 TYR 0.011 0.001 TYR B 59 ARG 0.018 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 159 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.783 Fit side-chains REVERT: R 6 THR cc_start: 0.8295 (OUTLIER) cc_final: 0.8017 (p) REVERT: R 120 ASN cc_start: 0.7790 (m110) cc_final: 0.7545 (m-40) REVERT: R 280 TYR cc_start: 0.8597 (p90) cc_final: 0.8267 (p90) REVERT: R 290 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7812 (tp40) REVERT: R 337 MET cc_start: 0.8188 (mtt) cc_final: 0.7911 (mtm) REVERT: R 370 ARG cc_start: 0.7269 (mtm-85) cc_final: 0.5559 (ptt90) REVERT: A 20 ASP cc_start: 0.7550 (m-30) cc_final: 0.7059 (m-30) REVERT: A 263 SER cc_start: 0.8851 (m) cc_final: 0.8606 (p) REVERT: A 306 GLN cc_start: 0.7494 (tp40) cc_final: 0.7127 (mm-40) REVERT: A 350 ASP cc_start: 0.7585 (m-30) cc_final: 0.7202 (m-30) REVERT: B 52 ARG cc_start: 0.8165 (mtt-85) cc_final: 0.7663 (ptp90) REVERT: B 201 SER cc_start: 0.9149 (OUTLIER) cc_final: 0.8938 (p) REVERT: B 249 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8260 (m) REVERT: B 268 ASN cc_start: 0.8180 (m110) cc_final: 0.7588 (t0) outliers start: 34 outliers final: 16 residues processed: 148 average time/residue: 0.9666 time to fit residues: 153.9282 Evaluate side-chains 138 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 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 B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 chunk 29 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 1 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.152828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.116977 restraints weight = 8128.102| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.19 r_work: 0.3262 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7279 Z= 0.194 Angle : 0.552 7.360 9903 Z= 0.286 Chirality : 0.041 0.185 1166 Planarity : 0.004 0.076 1241 Dihedral : 4.046 25.744 995 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.80 % Allowed : 22.25 % 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 (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: 0.37 (0.28), residues: 924 helix: 1.69 (0.27), residues: 377 sheet: -0.61 (0.33), residues: 216 loop : -0.75 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 182 HIS 0.005 0.001 HIS B 142 PHE 0.013 0.001 PHE B 292 TYR 0.013 0.001 TYR R 27 ARG 0.019 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 151 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.822 Fit side-chains REVERT: R 6 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8045 (p) REVERT: R 120 ASN cc_start: 0.7783 (m110) cc_final: 0.7560 (m-40) REVERT: R 280 TYR cc_start: 0.8635 (p90) cc_final: 0.8302 (p90) REVERT: R 290 GLN cc_start: 0.8419 (tm-30) cc_final: 0.7875 (tp40) REVERT: R 291 THR cc_start: 0.9179 (t) cc_final: 0.8928 (m) REVERT: R 370 ARG cc_start: 0.7306 (mtm-85) cc_final: 0.5635 (ptt90) REVERT: A 20 ASP cc_start: 0.7571 (m-30) cc_final: 0.7114 (m-30) REVERT: A 263 SER cc_start: 0.8860 (m) cc_final: 0.8649 (p) REVERT: A 306 GLN cc_start: 0.7416 (tp40) cc_final: 0.7006 (mm-40) REVERT: A 350 ASP cc_start: 0.7622 (m-30) cc_final: 0.7228 (m-30) REVERT: B 52 ARG cc_start: 0.8163 (mtt-85) cc_final: 0.7691 (ptp90) REVERT: B 249 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8290 (m) REVERT: B 268 ASN cc_start: 0.8431 (m110) cc_final: 0.7743 (t0) outliers start: 28 outliers final: 18 residues processed: 145 average time/residue: 0.9659 time to fit residues: 150.0387 Evaluate side-chains 139 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 35 SER Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 386 CYS Chi-restraints excluded: chain R residue 387 CYS Chi-restraints excluded: chain R residue 391 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 56 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 chunk 91 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 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** B 142 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.152346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.116042 restraints weight = 8183.888| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.22 r_work: 0.3190 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7279 Z= 0.220 Angle : 0.561 7.123 9903 Z= 0.291 Chirality : 0.041 0.187 1166 Planarity : 0.004 0.056 1241 Dihedral : 4.038 25.350 995 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.39 % Allowed : 23.20 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.28), residues: 924 helix: 1.72 (0.27), residues: 378 sheet: -0.62 (0.33), residues: 207 loop : -0.79 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 182 HIS 0.005 0.001 HIS B 142 PHE 0.016 0.001 PHE B 292 TYR 0.020 0.001 TYR R 347 ARG 0.013 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 150 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.808 Fit side-chains REVERT: R 6 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8086 (p) REVERT: R 120 ASN cc_start: 0.7760 (m110) cc_final: 0.7529 (m-40) REVERT: R 280 TYR cc_start: 0.8624 (p90) cc_final: 0.8284 (p90) REVERT: R 290 GLN cc_start: 0.8436 (tm-30) cc_final: 0.7820 (tp40) REVERT: R 291 THR cc_start: 0.9174 (t) cc_final: 0.8918 (m) REVERT: R 370 ARG cc_start: 0.7317 (mtm-85) cc_final: 0.5567 (ptt90) REVERT: R 384 THR cc_start: 0.8902 (m) cc_final: 0.8674 (t) REVERT: A 20 ASP cc_start: 0.7598 (m-30) cc_final: 0.7119 (m-30) REVERT: A 263 SER cc_start: 0.8851 (m) cc_final: 0.8605 (p) REVERT: A 306 GLN cc_start: 0.7387 (tp40) cc_final: 0.6982 (mm-40) REVERT: A 350 ASP cc_start: 0.7483 (m-30) cc_final: 0.7107 (m-30) REVERT: B 52 ARG cc_start: 0.8098 (mtt-85) cc_final: 0.7634 (ptp90) REVERT: B 249 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8265 (m) REVERT: B 268 ASN cc_start: 0.8400 (m110) cc_final: 0.7717 (t0) REVERT: B 325 MET cc_start: 0.7908 (tpt) cc_final: 0.7689 (tpp) outliers start: 25 outliers final: 20 residues processed: 142 average time/residue: 0.9235 time to fit residues: 140.4915 Evaluate side-chains 142 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 133 TYR Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 386 CYS Chi-restraints excluded: chain R residue 387 CYS Chi-restraints excluded: chain R residue 391 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 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: 0.6980 chunk 57 optimal weight: 30.0000 chunk 44 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.152630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.116184 restraints weight = 8294.056| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.25 r_work: 0.3194 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7279 Z= 0.222 Angle : 0.566 7.187 9903 Z= 0.294 Chirality : 0.042 0.200 1166 Planarity : 0.004 0.058 1241 Dihedral : 4.032 25.401 995 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.12 % Allowed : 23.47 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.28), residues: 924 helix: 1.70 (0.27), residues: 379 sheet: -0.60 (0.33), residues: 207 loop : -0.75 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 182 HIS 0.003 0.001 HIS B 183 PHE 0.016 0.001 PHE R 181 TYR 0.024 0.001 TYR R 347 ARG 0.014 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 142 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.759 Fit side-chains REVERT: R 6 THR cc_start: 0.8432 (OUTLIER) cc_final: 0.8117 (p) REVERT: R 120 ASN cc_start: 0.7846 (m110) cc_final: 0.7609 (m-40) REVERT: R 280 TYR cc_start: 0.8620 (p90) cc_final: 0.8269 (p90) REVERT: R 290 GLN cc_start: 0.8448 (tm-30) cc_final: 0.7848 (tp40) REVERT: R 291 THR cc_start: 0.9161 (t) cc_final: 0.8922 (m) REVERT: R 370 ARG cc_start: 0.7316 (mtm-85) cc_final: 0.5580 (ptt90) REVERT: R 384 THR cc_start: 0.8833 (m) cc_final: 0.8591 (t) REVERT: A 20 ASP cc_start: 0.7603 (m-30) cc_final: 0.7140 (m-30) REVERT: A 263 SER cc_start: 0.8855 (m) cc_final: 0.8614 (p) REVERT: A 306 GLN cc_start: 0.7336 (tp40) cc_final: 0.6925 (mm-40) REVERT: A 350 ASP cc_start: 0.7559 (m-30) cc_final: 0.7212 (m-30) REVERT: B 52 ARG cc_start: 0.8046 (mtt-85) cc_final: 0.7601 (ptp90) REVERT: B 249 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8268 (m) REVERT: B 268 ASN cc_start: 0.8315 (m110) cc_final: 0.7716 (t0) REVERT: B 325 MET cc_start: 0.7872 (tpt) cc_final: 0.7653 (tpp) outliers start: 23 outliers final: 18 residues processed: 135 average time/residue: 0.9619 time to fit residues: 138.8408 Evaluate side-chains 138 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 35 SER Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 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 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: 5.9990 chunk 56 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 11 optimal weight: 0.0870 chunk 74 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.151964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.115732 restraints weight = 8148.519| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.18 r_work: 0.3228 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7279 Z= 0.241 Angle : 0.575 7.045 9903 Z= 0.299 Chirality : 0.042 0.192 1166 Planarity : 0.004 0.059 1241 Dihedral : 4.068 25.308 995 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.53 % Allowed : 22.93 % 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: 1.72 (0.27), residues: 378 sheet: -0.60 (0.33), residues: 207 loop : -0.72 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP R 182 HIS 0.003 0.001 HIS B 183 PHE 0.020 0.001 PHE R 181 TYR 0.021 0.001 TYR R 347 ARG 0.014 0.001 ARG B 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5489.24 seconds wall clock time: 97 minutes 40.45 seconds (5860.45 seconds total)