Starting phenix.real_space_refine on Fri Aug 22 18:47:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ugy_42241/08_2025/8ugy_42241.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ugy_42241/08_2025/8ugy_42241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ugy_42241/08_2025/8ugy_42241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ugy_42241/08_2025/8ugy_42241.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ugy_42241/08_2025/8ugy_42241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ugy_42241/08_2025/8ugy_42241.map" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 4503 2.51 5 N 1159 2.21 5 O 1256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6970 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1750 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2558 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain: "G" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 391 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 4, 'TRANS': 45} Chain: "R" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2110 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "R" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 161 Unusual residues: {'CLR': 5, 'WRU': 1} Classifications: {'undetermined': 6, 'water': 1} Link IDs: {None: 6} Time building chain proxies: 1.67, per 1000 atoms: 0.24 Number of scatterers: 6970 At special positions: 0 Unit cell: (76.968, 99.417, 124.004, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1256 8.00 N 1159 7.00 C 4503 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 173 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 288.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1642 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 8 sheets defined 48.4% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.064A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.604A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.286A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.035A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.817A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.618A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 328 through 351 removed outlier: 3.585A pdb=" N CYS A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 26 removed outlier: 4.225A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 14 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'R' and resid 21 through 50 removed outlier: 3.571A pdb=" N THR R 37 " --> pdb=" O THR R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 75 Processing helix chain 'R' and resid 75 through 85 Processing helix chain 'R' and resid 93 through 126 removed outlier: 3.890A pdb=" N ILE R 110 " --> pdb=" O CYS R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 134 removed outlier: 4.308A pdb=" N ARG R 132 " --> pdb=" O ILE R 128 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS R 133 " --> pdb=" O GLU R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 153 Processing helix chain 'R' and resid 155 through 160 removed outlier: 3.843A pdb=" N PHE R 159 " --> pdb=" O MET R 155 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TRP R 160 " --> pdb=" O PRO R 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 155 through 160' Processing helix chain 'R' and resid 179 through 191 Processing helix chain 'R' and resid 191 through 215 removed outlier: 3.550A pdb=" N LYS R 215 " --> pdb=" O SER R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 316 removed outlier: 3.625A pdb=" N PHE R 300 " --> pdb=" O ILE R 296 " (cutoff:3.500A) Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 322 through 335 Processing helix chain 'R' and resid 335 through 346 Proline residue: R 341 - end of helix Processing helix chain 'R' and resid 348 through 358 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 52 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.322A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.243A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.564A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.530A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.581A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.637A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1134 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.08 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2185 1.35 - 1.47: 1700 1.47 - 1.59: 3161 1.59 - 1.71: 0 1.71 - 1.83: 74 Bond restraints: 7120 Sorted by residual: bond pdb=" C3 CLR R 404 " pdb=" O1 CLR R 404 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" C3 CLR R 403 " pdb=" O1 CLR R 403 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.16e+00 bond pdb=" C3 CLR R 405 " pdb=" O1 CLR R 405 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.14e+00 bond pdb=" C3 CLR R 402 " pdb=" O1 CLR R 402 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.12e+00 bond pdb=" C3 CLR R 401 " pdb=" O1 CLR R 401 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.07e+00 ... (remaining 7115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 9373 1.34 - 2.69: 230 2.69 - 4.03: 42 4.03 - 5.37: 20 5.37 - 6.71: 7 Bond angle restraints: 9672 Sorted by residual: angle pdb=" N GLU A 308 " pdb=" CA GLU A 308 " pdb=" CB GLU A 308 " ideal model delta sigma weight residual 110.39 114.73 -4.34 1.66e+00 3.63e-01 6.83e+00 angle pdb=" C PHE A 307 " pdb=" N GLU A 308 " pdb=" CA GLU A 308 " ideal model delta sigma weight residual 120.72 116.59 4.13 1.67e+00 3.59e-01 6.12e+00 angle pdb=" C VAL R 115 " pdb=" CA VAL R 115 " pdb=" CB VAL R 115 " ideal model delta sigma weight residual 112.16 108.22 3.94 1.63e+00 3.76e-01 5.83e+00 angle pdb=" N MET R 155 " pdb=" CA MET R 155 " pdb=" C MET R 155 " ideal model delta sigma weight residual 109.81 114.96 -5.15 2.21e+00 2.05e-01 5.44e+00 angle pdb=" N PRO R 156 " pdb=" CA PRO R 156 " pdb=" C PRO R 156 " ideal model delta sigma weight residual 110.70 113.54 -2.84 1.22e+00 6.72e-01 5.40e+00 ... (remaining 9667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.48: 4236 24.48 - 48.96: 223 48.96 - 73.43: 22 73.43 - 97.91: 2 97.91 - 122.39: 7 Dihedral angle restraints: 4490 sinusoidal: 1963 harmonic: 2527 Sorted by residual: dihedral pdb=" CB CYS R 95 " pdb=" SG CYS R 95 " pdb=" SG CYS R 173 " pdb=" CB CYS R 173 " ideal model delta sinusoidal sigma weight residual 93.00 179.63 -86.63 1 1.00e+01 1.00e-02 9.04e+01 dihedral pdb=" C1 CLR R 405 " pdb=" C2 CLR R 405 " pdb=" C3 CLR R 405 " pdb=" O1 CLR R 405 " ideal model delta sinusoidal sigma weight residual 180.04 57.65 122.39 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" N1 WRU R 406 " pdb=" C11 WRU R 406 " pdb=" C12 WRU R 406 " pdb=" N2 WRU R 406 " ideal model delta sinusoidal sigma weight residual -58.38 62.28 -120.66 1 3.00e+01 1.11e-03 1.61e+01 ... (remaining 4487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 748 0.037 - 0.074: 284 0.074 - 0.111: 79 0.111 - 0.148: 19 0.148 - 0.185: 2 Chirality restraints: 1132 Sorted by residual: chirality pdb=" C9 CLR R 402 " pdb=" C10 CLR R 402 " pdb=" C11 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.45 -2.26 -0.18 2.00e-01 2.50e+01 8.52e-01 chirality pdb=" CA ILE B 81 " pdb=" N ILE B 81 " pdb=" C ILE B 81 " pdb=" CB ILE B 81 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 1129 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET R 155 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO R 156 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO R 156 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 156 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C13 WRU R 406 " -0.005 2.00e-02 2.50e+03 1.20e-02 2.90e+00 pdb=" C14 WRU R 406 " 0.009 2.00e-02 2.50e+03 pdb=" C15 WRU R 406 " 0.011 2.00e-02 2.50e+03 pdb=" C16 WRU R 406 " -0.001 2.00e-02 2.50e+03 pdb=" C17 WRU R 406 " -0.014 2.00e-02 2.50e+03 pdb=" C18 WRU R 406 " -0.012 2.00e-02 2.50e+03 pdb=" C2 WRU R 406 " 0.022 2.00e-02 2.50e+03 pdb=" N2 WRU R 406 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " 0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO G 55 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " 0.019 5.00e-02 4.00e+02 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 132 2.69 - 3.24: 6786 3.24 - 3.80: 10978 3.80 - 4.35: 14659 4.35 - 4.90: 24924 Nonbonded interactions: 57479 Sorted by model distance: nonbonded pdb=" O PRO R 341 " pdb=" OG1 THR R 345 " model vdw 2.138 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.220 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.273 3.040 nonbonded pdb=" NE2 HIS B 225 " pdb=" OG1 THR B 243 " model vdw 2.274 3.120 nonbonded pdb=" OD1 ASP A 341 " pdb=" NZ LYS A 345 " model vdw 2.288 3.120 ... (remaining 57474 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.290 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 : 0.003 0.032 7122 Z= 0.143 Angle : 0.561 6.713 9676 Z= 0.290 Chirality : 0.043 0.185 1132 Planarity : 0.003 0.056 1170 Dihedral : 14.646 122.390 2842 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.71 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.29), residues: 848 helix: 1.66 (0.28), residues: 372 sheet: -0.64 (0.39), residues: 167 loop : -0.96 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 197 TYR 0.014 0.001 TYR R 203 PHE 0.012 0.001 PHE A 189 TRP 0.014 0.001 TRP B 82 HIS 0.001 0.000 HIS R 177 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 7120) covalent geometry : angle 0.56011 ( 9672) SS BOND : bond 0.00761 ( 2) SS BOND : angle 1.45232 ( 4) hydrogen bonds : bond 0.14685 ( 392) hydrogen bonds : angle 5.90784 ( 1134) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.263 Fit side-chains REVERT: A 349 LYS cc_start: 0.8582 (ttpt) cc_final: 0.8030 (ttmt) REVERT: R 338 LEU cc_start: 0.8846 (tp) cc_final: 0.8571 (tp) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.0735 time to fit residues: 12.0697 Evaluate side-chains 109 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0010 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 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 = 0.3532 r_free = 0.3532 target = 0.144063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.106774 restraints weight = 7853.322| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.98 r_work: 0.2953 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7122 Z= 0.157 Angle : 0.572 7.600 9676 Z= 0.293 Chirality : 0.042 0.159 1132 Planarity : 0.004 0.055 1170 Dihedral : 5.761 57.825 1274 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.83 % Favored : 97.05 % Rotamer: Outliers : 0.95 % Allowed : 8.92 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.29), residues: 848 helix: 1.94 (0.27), residues: 377 sheet: -0.65 (0.39), residues: 175 loop : -0.94 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.013 0.001 TYR R 203 PHE 0.013 0.001 PHE A 189 TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS R 207 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 7120) covalent geometry : angle 0.57131 ( 9672) SS BOND : bond 0.00857 ( 2) SS BOND : angle 1.69392 ( 4) hydrogen bonds : bond 0.03996 ( 392) hydrogen bonds : angle 4.59315 ( 1134) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.244 Fit side-chains REVERT: A 255 ASN cc_start: 0.8502 (m110) cc_final: 0.8289 (m-40) REVERT: A 349 LYS cc_start: 0.8425 (ttpt) cc_final: 0.7912 (ttmt) REVERT: R 85 MET cc_start: 0.7186 (mtp) cc_final: 0.6927 (mmm) REVERT: R 124 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8101 (mp) REVERT: R 338 LEU cc_start: 0.8783 (tp) cc_final: 0.8432 (tp) outliers start: 7 outliers final: 4 residues processed: 112 average time/residue: 0.0845 time to fit residues: 12.3316 Evaluate side-chains 112 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain R residue 45 MET Chi-restraints excluded: chain R residue 124 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 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 = 0.3529 r_free = 0.3529 target = 0.144214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.105475 restraints weight = 7764.369| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.11 r_work: 0.2924 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7122 Z= 0.143 Angle : 0.517 6.114 9676 Z= 0.273 Chirality : 0.041 0.151 1132 Planarity : 0.004 0.056 1170 Dihedral : 5.097 58.329 1274 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.59 % Favored : 97.29 % Rotamer: Outliers : 1.76 % Allowed : 11.35 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.30), residues: 848 helix: 2.01 (0.27), residues: 380 sheet: -0.72 (0.39), residues: 182 loop : -0.88 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.014 0.001 TYR R 182 PHE 0.013 0.001 PHE A 189 TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS R 207 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 7120) covalent geometry : angle 0.51601 ( 9672) SS BOND : bond 0.00881 ( 2) SS BOND : angle 1.66167 ( 4) hydrogen bonds : bond 0.03592 ( 392) hydrogen bonds : angle 4.48469 ( 1134) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.246 Fit side-chains REVERT: A 255 ASN cc_start: 0.8569 (m110) cc_final: 0.8287 (m-40) REVERT: A 349 LYS cc_start: 0.8563 (ttpt) cc_final: 0.8049 (ttmt) REVERT: R 124 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8292 (mt) REVERT: R 338 LEU cc_start: 0.8806 (tp) cc_final: 0.8408 (tp) outliers start: 13 outliers final: 10 residues processed: 117 average time/residue: 0.0843 time to fit residues: 12.9599 Evaluate side-chains 119 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 45 MET Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 321 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 64 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 50 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 10 optimal weight: 0.0670 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 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 = 0.3536 r_free = 0.3536 target = 0.144787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.106765 restraints weight = 7736.723| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.06 r_work: 0.2946 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7122 Z= 0.122 Angle : 0.490 6.035 9676 Z= 0.260 Chirality : 0.041 0.145 1132 Planarity : 0.003 0.055 1170 Dihedral : 5.079 57.308 1274 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.18 % Favored : 96.70 % Rotamer: Outliers : 2.84 % Allowed : 12.57 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.30), residues: 848 helix: 2.11 (0.27), residues: 380 sheet: -0.69 (0.39), residues: 185 loop : -0.86 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.014 0.001 TYR R 182 PHE 0.012 0.001 PHE A 189 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS R 207 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7120) covalent geometry : angle 0.48923 ( 9672) SS BOND : bond 0.00776 ( 2) SS BOND : angle 1.48488 ( 4) hydrogen bonds : bond 0.03327 ( 392) hydrogen bonds : angle 4.37591 ( 1134) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.216 Fit side-chains REVERT: A 255 ASN cc_start: 0.8618 (m110) cc_final: 0.8360 (m-40) REVERT: A 275 GLU cc_start: 0.8793 (tt0) cc_final: 0.8547 (tt0) REVERT: A 349 LYS cc_start: 0.8588 (ttpt) cc_final: 0.8092 (ttmt) REVERT: G 19 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7791 (tt) REVERT: R 124 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8078 (mp) REVERT: R 338 LEU cc_start: 0.8802 (tp) cc_final: 0.8355 (tp) outliers start: 21 outliers final: 12 residues processed: 127 average time/residue: 0.0751 time to fit residues: 12.5762 Evaluate side-chains 121 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 45 MET Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 321 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.142367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.104332 restraints weight = 7849.938| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.03 r_work: 0.2927 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7122 Z= 0.176 Angle : 0.540 6.091 9676 Z= 0.284 Chirality : 0.042 0.151 1132 Planarity : 0.003 0.054 1170 Dihedral : 5.278 56.263 1274 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.30 % Favored : 96.58 % Rotamer: Outliers : 2.84 % Allowed : 13.38 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.30), residues: 848 helix: 1.96 (0.27), residues: 387 sheet: -0.78 (0.39), residues: 179 loop : -0.90 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 197 TYR 0.014 0.001 TYR R 182 PHE 0.015 0.001 PHE A 189 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS R 207 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 7120) covalent geometry : angle 0.53860 ( 9672) SS BOND : bond 0.01018 ( 2) SS BOND : angle 1.93333 ( 4) hydrogen bonds : bond 0.03616 ( 392) hydrogen bonds : angle 4.50003 ( 1134) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.176 Fit side-chains REVERT: A 349 LYS cc_start: 0.8610 (ttpt) cc_final: 0.8109 (ttmt) REVERT: B 20 ASP cc_start: 0.8112 (m-30) cc_final: 0.7806 (m-30) REVERT: G 19 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7788 (tt) REVERT: R 124 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8088 (mp) REVERT: R 212 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6434 (mp) REVERT: R 338 LEU cc_start: 0.8789 (tp) cc_final: 0.8303 (tp) outliers start: 21 outliers final: 14 residues processed: 124 average time/residue: 0.0771 time to fit residues: 12.6944 Evaluate side-chains 127 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 45 MET Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 312 LEU Chi-restraints excluded: chain R residue 321 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.142150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.104668 restraints weight = 7937.121| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.07 r_work: 0.2912 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7122 Z= 0.146 Angle : 0.522 6.012 9676 Z= 0.275 Chirality : 0.042 0.143 1132 Planarity : 0.003 0.053 1170 Dihedral : 5.256 55.634 1274 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.30 % Favored : 96.58 % Rotamer: Outliers : 2.97 % Allowed : 15.14 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.30), residues: 848 helix: 2.02 (0.27), residues: 387 sheet: -0.76 (0.39), residues: 179 loop : -0.86 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.013 0.001 TYR R 182 PHE 0.013 0.001 PHE A 189 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 207 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 7120) covalent geometry : angle 0.52120 ( 9672) SS BOND : bond 0.00901 ( 2) SS BOND : angle 1.68892 ( 4) hydrogen bonds : bond 0.03432 ( 392) hydrogen bonds : angle 4.43266 ( 1134) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.240 Fit side-chains REVERT: A 229 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7776 (t0) REVERT: A 275 GLU cc_start: 0.8752 (tt0) cc_final: 0.8315 (tt0) REVERT: A 349 LYS cc_start: 0.8612 (ttpt) cc_final: 0.8124 (ttmt) REVERT: B 20 ASP cc_start: 0.8029 (m-30) cc_final: 0.7690 (m-30) REVERT: B 234 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.9004 (m-80) REVERT: G 19 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7714 (tt) REVERT: R 124 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8079 (mp) REVERT: R 212 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6391 (mp) REVERT: R 338 LEU cc_start: 0.8737 (tp) cc_final: 0.8215 (tp) outliers start: 22 outliers final: 14 residues processed: 126 average time/residue: 0.0939 time to fit residues: 15.6429 Evaluate side-chains 130 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 45 MET Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 321 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 57 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 0.0570 chunk 78 optimal weight: 3.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.147598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.110112 restraints weight = 7719.440| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.07 r_work: 0.2925 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7122 Z= 0.125 Angle : 0.507 5.918 9676 Z= 0.267 Chirality : 0.041 0.139 1132 Planarity : 0.003 0.052 1170 Dihedral : 5.198 55.018 1274 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.30 % Favored : 96.58 % Rotamer: Outliers : 3.24 % Allowed : 15.95 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.30), residues: 848 helix: 2.09 (0.27), residues: 387 sheet: -0.74 (0.40), residues: 177 loop : -0.85 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.014 0.001 TYR R 182 PHE 0.012 0.001 PHE A 189 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7120) covalent geometry : angle 0.50607 ( 9672) SS BOND : bond 0.00769 ( 2) SS BOND : angle 1.46792 ( 4) hydrogen bonds : bond 0.03297 ( 392) hydrogen bonds : angle 4.36200 ( 1134) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.242 Fit side-chains REVERT: A 229 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7776 (t0) REVERT: A 349 LYS cc_start: 0.8627 (ttpt) cc_final: 0.8142 (ttmt) REVERT: B 20 ASP cc_start: 0.8082 (m-30) cc_final: 0.7733 (m-30) REVERT: B 234 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.8907 (m-80) REVERT: G 19 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7714 (tt) REVERT: R 124 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8091 (mp) REVERT: R 212 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6365 (mp) REVERT: R 338 LEU cc_start: 0.8766 (tp) cc_final: 0.8233 (tp) outliers start: 24 outliers final: 13 residues processed: 125 average time/residue: 0.0857 time to fit residues: 14.0393 Evaluate side-chains 130 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 45 MET Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 321 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 80 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.147557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.109939 restraints weight = 7782.950| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.07 r_work: 0.2985 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7122 Z= 0.157 Angle : 0.531 6.010 9676 Z= 0.279 Chirality : 0.042 0.142 1132 Planarity : 0.003 0.052 1170 Dihedral : 5.283 54.062 1274 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.42 % Favored : 96.46 % Rotamer: Outliers : 2.84 % Allowed : 16.22 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.30), residues: 848 helix: 2.03 (0.27), residues: 387 sheet: -0.79 (0.40), residues: 177 loop : -0.85 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 197 TYR 0.015 0.001 TYR R 182 PHE 0.014 0.001 PHE A 189 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 7120) covalent geometry : angle 0.52949 ( 9672) SS BOND : bond 0.00938 ( 2) SS BOND : angle 1.79040 ( 4) hydrogen bonds : bond 0.03444 ( 392) hydrogen bonds : angle 4.44851 ( 1134) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.268 Fit side-chains REVERT: A 229 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7830 (t0) REVERT: A 349 LYS cc_start: 0.8712 (ttpt) cc_final: 0.8215 (ttmt) REVERT: B 234 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8957 (m-80) REVERT: G 19 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7785 (tt) REVERT: R 124 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8177 (mp) REVERT: R 212 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6526 (mp) outliers start: 21 outliers final: 13 residues processed: 121 average time/residue: 0.0701 time to fit residues: 11.4124 Evaluate side-chains 129 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 45 MET Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 312 LEU Chi-restraints excluded: chain R residue 321 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.142959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.104901 restraints weight = 7865.344| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.10 r_work: 0.2974 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7122 Z= 0.133 Angle : 0.529 6.214 9676 Z= 0.278 Chirality : 0.041 0.137 1132 Planarity : 0.003 0.052 1170 Dihedral : 5.231 53.367 1274 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.07 % Favored : 96.82 % Rotamer: Outliers : 2.84 % Allowed : 16.76 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.30), residues: 848 helix: 2.09 (0.27), residues: 386 sheet: -0.75 (0.40), residues: 177 loop : -0.85 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.014 0.001 TYR R 182 PHE 0.013 0.001 PHE A 189 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 7120) covalent geometry : angle 0.52828 ( 9672) SS BOND : bond 0.00791 ( 2) SS BOND : angle 1.52770 ( 4) hydrogen bonds : bond 0.03302 ( 392) hydrogen bonds : angle 4.39773 ( 1134) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.249 Fit side-chains REVERT: A 229 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7807 (t0) REVERT: A 349 LYS cc_start: 0.8713 (ttpt) cc_final: 0.8216 (ttmt) REVERT: B 20 ASP cc_start: 0.8122 (m-30) cc_final: 0.7759 (m-30) REVERT: B 234 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.8920 (m-80) REVERT: G 19 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7764 (tt) REVERT: R 124 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8161 (mp) REVERT: R 212 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6508 (mp) REVERT: R 338 LEU cc_start: 0.8847 (tp) cc_final: 0.8525 (tp) outliers start: 21 outliers final: 14 residues processed: 126 average time/residue: 0.0790 time to fit residues: 13.0480 Evaluate side-chains 130 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 45 MET Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 312 LEU Chi-restraints excluded: chain R residue 321 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 67 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 83 optimal weight: 0.0970 chunk 51 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.142739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.104846 restraints weight = 7812.713| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.04 r_work: 0.2989 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7122 Z= 0.154 Angle : 0.542 6.949 9676 Z= 0.284 Chirality : 0.042 0.139 1132 Planarity : 0.003 0.052 1170 Dihedral : 5.272 52.284 1274 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.30 % Favored : 96.58 % Rotamer: Outliers : 2.70 % Allowed : 17.03 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.30), residues: 848 helix: 2.02 (0.27), residues: 387 sheet: -0.80 (0.40), residues: 177 loop : -0.83 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 197 TYR 0.013 0.001 TYR R 182 PHE 0.014 0.001 PHE A 189 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 7120) covalent geometry : angle 0.54128 ( 9672) SS BOND : bond 0.00912 ( 2) SS BOND : angle 1.73891 ( 4) hydrogen bonds : bond 0.03421 ( 392) hydrogen bonds : angle 4.44293 ( 1134) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.248 Fit side-chains REVERT: A 229 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7755 (t0) REVERT: A 349 LYS cc_start: 0.8679 (ttpt) cc_final: 0.8191 (ttmt) REVERT: B 234 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.8945 (m-80) REVERT: G 19 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7679 (tt) REVERT: R 124 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8124 (mp) REVERT: R 212 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6442 (mp) REVERT: R 338 LEU cc_start: 0.8824 (tp) cc_final: 0.8498 (tp) outliers start: 20 outliers final: 14 residues processed: 121 average time/residue: 0.0718 time to fit residues: 11.6180 Evaluate side-chains 131 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 45 MET Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 312 LEU Chi-restraints excluded: chain R residue 321 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 53 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 8 optimal weight: 0.0770 chunk 10 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.146361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.108247 restraints weight = 7695.246| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.13 r_work: 0.2946 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7122 Z= 0.126 Angle : 0.526 6.521 9676 Z= 0.276 Chirality : 0.041 0.136 1132 Planarity : 0.003 0.052 1170 Dihedral : 5.199 51.797 1274 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.30 % Favored : 96.58 % Rotamer: Outliers : 2.84 % Allowed : 17.03 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.30), residues: 848 helix: 2.11 (0.27), residues: 387 sheet: -0.77 (0.39), residues: 185 loop : -0.75 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 197 TYR 0.012 0.001 TYR R 182 PHE 0.012 0.001 PHE A 189 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7120) covalent geometry : angle 0.52551 ( 9672) SS BOND : bond 0.00753 ( 2) SS BOND : angle 1.46310 ( 4) hydrogen bonds : bond 0.03232 ( 392) hydrogen bonds : angle 4.35507 ( 1134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1726.72 seconds wall clock time: 30 minutes 18.30 seconds (1818.30 seconds total)