Starting phenix.real_space_refine on Wed Mar 12 01:12:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ugy_42241/03_2025/8ugy_42241.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ugy_42241/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ugy_42241/03_2025/8ugy_42241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ugy_42241/03_2025/8ugy_42241.map" model { file = "/net/cci-nas-00/data/ceres_data/8ugy_42241/03_2025/8ugy_42241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ugy_42241/03_2025/8ugy_42241.cif" } resolution = 3.31 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= -0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.77, per 1000 atoms: 0.68 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: 1.77 Conformation dependent library (CDL) restraints added in 959.7 milliseconds 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: 0.71 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: 1.83 Time building geometry restraints manager: 2.07 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.560 Find NCS groups from input model: 0.060 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.960 ------------------------------------------------------------------------------- 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 7120 Z= 0.208 Angle : 0.560 6.713 9672 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 : 7.35 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 (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: 0.36 (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 TRP 0.014 0.001 TRP B 82 HIS 0.001 0.000 HIS R 177 PHE 0.012 0.001 PHE A 189 TYR 0.014 0.001 TYR R 203 ARG 0.007 0.000 ARG B 197 *********************** 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 : 0.743 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: 0.2265 time to fit residues: 36.7388 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 : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 0.0020 chunk 34 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.0270 chunk 49 optimal weight: 0.0870 chunk 77 optimal weight: 0.7980 overall best weight: 0.3424 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.147614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.110390 restraints weight = 7733.544| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.99 r_work: 0.3087 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7120 Z= 0.163 Angle : 0.536 6.496 9672 Z= 0.277 Chirality : 0.041 0.154 1132 Planarity : 0.004 0.055 1170 Dihedral : 5.410 56.889 1274 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.07 % Favored : 96.82 % Rotamer: Outliers : 1.08 % Allowed : 8.24 % Favored : 90.68 % 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: 0.70 (0.30), residues: 848 helix: 2.09 (0.27), residues: 376 sheet: -0.65 (0.38), residues: 183 loop : -0.93 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS R 207 PHE 0.011 0.001 PHE R 300 TYR 0.012 0.001 TYR R 182 ARG 0.007 0.000 ARG B 19 *********************** 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 124 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.750 Fit side-chains REVERT: A 255 ASN cc_start: 0.8635 (m110) cc_final: 0.8418 (m-40) REVERT: A 349 LYS cc_start: 0.8596 (ttpt) cc_final: 0.8079 (ttmt) REVERT: R 124 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8243 (mp) outliers start: 8 outliers final: 5 residues processed: 117 average time/residue: 0.2265 time to fit residues: 34.5346 Evaluate side-chains 116 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 101 MET 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 41 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 17 optimal weight: 0.2980 chunk 47 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.145176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.107212 restraints weight = 7809.256| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.08 r_work: 0.2947 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7120 Z= 0.201 Angle : 0.503 6.052 9672 Z= 0.266 Chirality : 0.041 0.153 1132 Planarity : 0.003 0.055 1170 Dihedral : 4.954 57.928 1274 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.59 % Favored : 97.29 % Rotamer: Outliers : 1.49 % Allowed : 10.95 % Favored : 87.57 % 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: 0.73 (0.30), residues: 848 helix: 2.11 (0.27), residues: 379 sheet: -0.70 (0.38), residues: 185 loop : -0.88 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS R 207 PHE 0.013 0.001 PHE A 189 TYR 0.013 0.001 TYR R 182 ARG 0.004 0.000 ARG B 19 *********************** 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 119 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.802 Fit side-chains REVERT: A 255 ASN cc_start: 0.8538 (m110) cc_final: 0.8277 (m-40) REVERT: A 349 LYS cc_start: 0.8529 (ttpt) cc_final: 0.8022 (ttmt) REVERT: A 353 LEU cc_start: 0.8178 (mt) cc_final: 0.7899 (mt) REVERT: R 124 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8148 (mt) REVERT: R 338 LEU cc_start: 0.8746 (tp) cc_final: 0.8500 (tp) outliers start: 11 outliers final: 8 residues processed: 111 average time/residue: 0.2077 time to fit residues: 30.3141 Evaluate side-chains 115 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 189 SER 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 0.0970 chunk 1 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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** R 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.144631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.106650 restraints weight = 7860.688| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.09 r_work: 0.2944 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7120 Z= 0.196 Angle : 0.494 6.016 9672 Z= 0.262 Chirality : 0.041 0.149 1132 Planarity : 0.003 0.054 1170 Dihedral : 5.017 56.987 1274 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.30 % Favored : 96.58 % Rotamer: Outliers : 2.57 % Allowed : 12.30 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.78 (0.30), residues: 848 helix: 2.14 (0.27), residues: 380 sheet: -0.68 (0.39), residues: 185 loop : -0.85 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS R 207 PHE 0.013 0.001 PHE A 189 TYR 0.013 0.001 TYR R 182 ARG 0.005 0.000 ARG B 19 *********************** 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 131 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.742 Fit side-chains REVERT: A 255 ASN cc_start: 0.8613 (m110) cc_final: 0.8338 (m-40) REVERT: A 275 GLU cc_start: 0.8730 (tt0) cc_final: 0.8468 (tt0) REVERT: A 349 LYS cc_start: 0.8582 (ttpt) cc_final: 0.8070 (ttmt) REVERT: A 353 LEU cc_start: 0.8284 (mt) cc_final: 0.8031 (mt) REVERT: G 19 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7812 (tt) REVERT: R 124 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8071 (mp) REVERT: R 338 LEU cc_start: 0.8773 (tp) cc_final: 0.8469 (tp) outliers start: 19 outliers final: 11 residues processed: 122 average time/residue: 0.2091 time to fit residues: 33.4267 Evaluate side-chains 122 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 33 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 101 MET 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 47 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 43 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 57 optimal weight: 0.0000 overall best weight: 0.4584 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.146842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.108040 restraints weight = 7726.400| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.18 r_work: 0.2945 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7120 Z= 0.169 Angle : 0.480 5.944 9672 Z= 0.256 Chirality : 0.040 0.142 1132 Planarity : 0.003 0.054 1170 Dihedral : 4.981 56.197 1274 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.07 % Favored : 96.82 % Rotamer: Outliers : 2.84 % Allowed : 12.97 % Favored : 84.19 % 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: 0.85 (0.30), residues: 848 helix: 2.20 (0.27), residues: 381 sheet: -0.68 (0.39), residues: 186 loop : -0.79 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS R 207 PHE 0.012 0.001 PHE A 189 TYR 0.013 0.001 TYR R 182 ARG 0.005 0.000 ARG B 197 *********************** 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 135 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.732 Fit side-chains REVERT: A 275 GLU cc_start: 0.8709 (tt0) cc_final: 0.8450 (tt0) REVERT: A 349 LYS cc_start: 0.8589 (ttpt) cc_final: 0.8093 (ttmt) REVERT: A 350 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8331 (t0) REVERT: A 353 LEU cc_start: 0.8257 (mt) cc_final: 0.7990 (mt) REVERT: B 20 ASP cc_start: 0.8043 (m-30) cc_final: 0.7750 (m-30) REVERT: G 19 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7794 (tt) REVERT: R 124 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8046 (mp) REVERT: R 212 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6241 (mp) REVERT: R 338 LEU cc_start: 0.8757 (tp) cc_final: 0.8415 (tp) outliers start: 21 outliers final: 12 residues processed: 125 average time/residue: 0.1967 time to fit residues: 32.5046 Evaluate side-chains 129 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 101 MET 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 321 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 74 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 80 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.143266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.105240 restraints weight = 7821.412| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.08 r_work: 0.3002 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7120 Z= 0.232 Angle : 0.513 5.998 9672 Z= 0.272 Chirality : 0.042 0.148 1132 Planarity : 0.003 0.053 1170 Dihedral : 5.097 55.319 1274 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.42 % Favored : 96.46 % Rotamer: Outliers : 2.70 % Allowed : 13.92 % Favored : 83.38 % 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: 0.71 (0.30), residues: 848 helix: 2.00 (0.27), residues: 389 sheet: -0.71 (0.39), residues: 177 loop : -0.86 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS R 207 PHE 0.014 0.001 PHE A 189 TYR 0.013 0.001 TYR R 182 ARG 0.005 0.000 ARG B 19 *********************** 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 132 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.827 Fit side-chains REVERT: A 275 GLU cc_start: 0.8773 (tt0) cc_final: 0.8359 (tt0) REVERT: A 349 LYS cc_start: 0.8726 (ttpt) cc_final: 0.8229 (ttmt) REVERT: B 20 ASP cc_start: 0.8049 (m-30) cc_final: 0.7708 (m-30) REVERT: G 19 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7826 (tt) REVERT: R 124 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8161 (mp) REVERT: R 212 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6451 (mp) outliers start: 20 outliers final: 13 residues processed: 122 average time/residue: 0.2053 time to fit residues: 33.2156 Evaluate side-chains 128 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 101 MET 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 321 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 79 optimal weight: 0.0870 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.144125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.105937 restraints weight = 7790.963| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.09 r_work: 0.2930 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7120 Z= 0.204 Angle : 0.505 5.921 9672 Z= 0.266 Chirality : 0.041 0.140 1132 Planarity : 0.003 0.052 1170 Dihedral : 5.096 54.594 1274 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.83 % Favored : 97.05 % Rotamer: Outliers : 3.24 % Allowed : 14.05 % Favored : 82.70 % 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: 0.76 (0.30), residues: 848 helix: 2.09 (0.27), residues: 388 sheet: -0.80 (0.38), residues: 186 loop : -0.80 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.013 0.001 PHE A 189 TYR 0.013 0.001 TYR R 182 ARG 0.006 0.000 ARG B 19 *********************** 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 134 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.753 Fit side-chains REVERT: A 229 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7660 (t0) REVERT: A 275 GLU cc_start: 0.8733 (tt0) cc_final: 0.8296 (tt0) REVERT: A 308 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: A 349 LYS cc_start: 0.8613 (ttpt) cc_final: 0.8134 (ttmt) REVERT: B 20 ASP cc_start: 0.8062 (m-30) cc_final: 0.7714 (m-30) REVERT: B 234 PHE cc_start: 0.9232 (OUTLIER) cc_final: 0.8970 (m-80) REVERT: G 19 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7715 (tt) REVERT: R 124 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8065 (mp) REVERT: R 212 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6325 (mp) REVERT: R 338 LEU cc_start: 0.8729 (tp) cc_final: 0.8374 (tp) outliers start: 24 outliers final: 12 residues processed: 122 average time/residue: 0.2050 time to fit residues: 33.0834 Evaluate side-chains 127 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 308 GLU 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 67 SER Chi-restraints excluded: chain B residue 101 MET 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 321 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 38 optimal weight: 0.0070 chunk 65 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 67 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 47 optimal weight: 0.0770 chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 overall best weight: 0.3556 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.146479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.108266 restraints weight = 7760.895| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.10 r_work: 0.2961 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7120 Z= 0.157 Angle : 0.486 5.848 9672 Z= 0.257 Chirality : 0.040 0.135 1132 Planarity : 0.003 0.052 1170 Dihedral : 4.989 53.781 1274 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.30 % Favored : 96.58 % Rotamer: Outliers : 2.70 % Allowed : 15.27 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.82 (0.30), residues: 848 helix: 2.15 (0.27), residues: 389 sheet: -0.77 (0.38), residues: 186 loop : -0.79 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS R 207 PHE 0.011 0.001 PHE A 189 TYR 0.014 0.001 TYR R 182 ARG 0.005 0.000 ARG B 19 *********************** 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 130 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.781 Fit side-chains REVERT: A 229 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7661 (t0) REVERT: A 275 GLU cc_start: 0.8772 (tt0) cc_final: 0.8343 (tt0) REVERT: A 349 LYS cc_start: 0.8606 (ttpt) cc_final: 0.8149 (ttmt) REVERT: A 350 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8337 (t0) REVERT: B 20 ASP cc_start: 0.8066 (m-30) cc_final: 0.7712 (m-30) REVERT: B 234 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8823 (m-80) REVERT: G 19 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7734 (tt) REVERT: R 124 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8061 (mp) REVERT: R 126 ASN cc_start: 0.8456 (t0) cc_final: 0.8203 (t0) REVERT: R 212 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6288 (tt) REVERT: R 338 LEU cc_start: 0.8780 (tp) cc_final: 0.8429 (tp) outliers start: 20 outliers final: 10 residues processed: 121 average time/residue: 0.2094 time to fit residues: 33.4420 Evaluate side-chains 123 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP 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 67 SER Chi-restraints excluded: chain B residue 101 MET 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 321 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 67 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 40 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.140915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.102014 restraints weight = 7900.183| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.11 r_work: 0.2880 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7120 Z= 0.355 Angle : 0.586 6.461 9672 Z= 0.306 Chirality : 0.044 0.150 1132 Planarity : 0.004 0.053 1170 Dihedral : 5.401 51.667 1274 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.18 % Favored : 96.70 % Rotamer: Outliers : 2.84 % Allowed : 15.27 % 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 (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: 0.64 (0.30), residues: 848 helix: 1.98 (0.27), residues: 387 sheet: -0.82 (0.39), residues: 179 loop : -0.86 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.018 0.002 PHE A 189 TYR 0.013 0.002 TYR R 182 ARG 0.005 0.000 ARG B 19 *********************** 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 135 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.712 Fit side-chains REVERT: A 229 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7809 (t0) REVERT: A 275 GLU cc_start: 0.8807 (tt0) cc_final: 0.8362 (tt0) REVERT: A 349 LYS cc_start: 0.8655 (ttpt) cc_final: 0.8159 (ttmt) REVERT: B 20 ASP cc_start: 0.8144 (m-30) cc_final: 0.7782 (m-30) REVERT: B 234 PHE cc_start: 0.9320 (OUTLIER) cc_final: 0.9075 (m-80) REVERT: G 19 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7743 (tt) REVERT: R 124 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8117 (mp) REVERT: R 212 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6345 (tt) REVERT: R 338 LEU cc_start: 0.8782 (tp) cc_final: 0.8417 (tp) outliers start: 21 outliers final: 12 residues processed: 126 average time/residue: 0.2006 time to fit residues: 33.5847 Evaluate side-chains 128 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP 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 67 SER Chi-restraints excluded: chain B residue 101 MET 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 94 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 6 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.143326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.104822 restraints weight = 7816.721| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.10 r_work: 0.2935 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 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 0.035 7120 Z= 0.209 Angle : 0.542 6.564 9672 Z= 0.282 Chirality : 0.042 0.140 1132 Planarity : 0.003 0.052 1170 Dihedral : 5.272 50.755 1274 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.18 % Favored : 96.70 % Rotamer: Outliers : 2.30 % Allowed : 16.35 % Favored : 81.35 % 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: 0.79 (0.30), residues: 848 helix: 2.12 (0.27), residues: 386 sheet: -0.70 (0.40), residues: 175 loop : -0.86 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.013 0.001 PHE A 189 TYR 0.014 0.001 TYR R 182 ARG 0.006 0.000 ARG B 19 ********************** 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 131 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.679 Fit side-chains REVERT: A 229 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7766 (t0) REVERT: A 275 GLU cc_start: 0.8822 (tt0) cc_final: 0.8369 (tt0) REVERT: A 349 LYS cc_start: 0.8676 (ttpt) cc_final: 0.8178 (ttmt) REVERT: B 20 ASP cc_start: 0.8132 (m-30) cc_final: 0.7771 (m-30) REVERT: B 234 PHE cc_start: 0.9261 (OUTLIER) cc_final: 0.8937 (m-80) REVERT: G 19 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7804 (tt) REVERT: R 124 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8111 (mp) REVERT: R 212 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6374 (tt) REVERT: R 338 LEU cc_start: 0.8816 (tp) cc_final: 0.8425 (tp) outliers start: 17 outliers final: 12 residues processed: 123 average time/residue: 0.2083 time to fit residues: 33.6530 Evaluate side-chains 128 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 67 SER Chi-restraints excluded: chain B residue 101 MET 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 94 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 43 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.142998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.105260 restraints weight = 7731.121| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.00 r_work: 0.2949 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7120 Z= 0.223 Angle : 0.546 7.066 9672 Z= 0.285 Chirality : 0.042 0.141 1132 Planarity : 0.003 0.052 1170 Dihedral : 5.244 49.505 1274 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.30 % Favored : 96.58 % Rotamer: Outliers : 2.57 % Allowed : 16.49 % 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 (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: 0.78 (0.30), residues: 848 helix: 2.09 (0.27), residues: 387 sheet: -0.71 (0.40), residues: 175 loop : -0.82 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.014 0.001 PHE A 189 TYR 0.013 0.001 TYR R 182 ARG 0.007 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4131.93 seconds wall clock time: 71 minutes 52.00 seconds (4312.00 seconds total)