Starting phenix.real_space_refine on Sat May 10 22:17:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ugy_42241/05_2025/8ugy_42241.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ugy_42241/05_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_42241/05_2025/8ugy_42241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ugy_42241/05_2025/8ugy_42241.map" model { file = "/net/cci-nas-00/data/ceres_data/8ugy_42241/05_2025/8ugy_42241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ugy_42241/05_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-5687/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: 4.90, per 1000 atoms: 0.70 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: 1.89 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.77 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: 2.06 Time building geometry restraints manager: 2.16 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: 1.400 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.400 Find NCS groups from input model: 0.070 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.240 ------------------------------------------------------------------------------- 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 : 7.35 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 Details of bonding type rmsd hydrogen bonds : bond 0.14685 ( 392) hydrogen bonds : angle 5.90784 ( 1134) SS BOND : bond 0.00761 ( 2) SS BOND : angle 1.45232 ( 4) covalent geometry : bond 0.00321 ( 7120) covalent geometry : angle 0.56011 ( 9672) *********************** 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 : 0.738 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: 0.2315 time to fit residues: 37.5045 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 : 0.678 ------------------------------------------------------------------------------- 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 = 7733.554| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.99 r_work: 0.3043 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 7122 Z= 0.115 Angle : 0.536 6.496 9676 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 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 392) hydrogen bonds : angle 4.47149 ( 1134) SS BOND : bond 0.00592 ( 2) SS BOND : angle 1.23156 ( 4) covalent geometry : bond 0.00253 ( 7120) covalent geometry : angle 0.53592 ( 9672) *********************** 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 : 0.773 Fit side-chains REVERT: A 255 ASN cc_start: 0.8623 (m110) cc_final: 0.8405 (m-40) REVERT: A 349 LYS cc_start: 0.8593 (ttpt) cc_final: 0.8081 (ttmt) REVERT: R 124 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8227 (mp) outliers start: 8 outliers final: 5 residues processed: 117 average time/residue: 0.2241 time to fit residues: 34.0131 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 : 0.792 ------------------------------------------------------------------------------- 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: 0.8980 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 47 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.145469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.107367 restraints weight = 7805.585| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.09 r_work: 0.2951 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7122 Z= 0.127 Angle : 0.500 6.051 9676 Z= 0.265 Chirality : 0.041 0.152 1132 Planarity : 0.003 0.055 1170 Dihedral : 4.945 58.038 1274 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.59 % Favored : 97.29 % Rotamer: Outliers : 1.35 % Allowed : 11.08 % 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: 0.74 (0.30), residues: 848 helix: 2.12 (0.27), residues: 379 sheet: -0.69 (0.38), residues: 185 loop : -0.88 (0.37), 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 0.014 0.001 TYR R 182 ARG 0.004 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03458 ( 392) hydrogen bonds : angle 4.39390 ( 1134) SS BOND : bond 0.00770 ( 2) SS BOND : angle 1.48639 ( 4) covalent geometry : bond 0.00293 ( 7120) covalent geometry : angle 0.49899 ( 9672) *********************** 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: 10 poor density : 109 time to evaluate : 0.777 Fit side-chains REVERT: A 255 ASN cc_start: 0.8550 (m110) cc_final: 0.8284 (m-40) REVERT: A 349 LYS cc_start: 0.8550 (ttpt) cc_final: 0.8039 (ttmt) REVERT: A 350 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8354 (t0) REVERT: A 353 LEU cc_start: 0.8190 (mt) cc_final: 0.7909 (mt) REVERT: R 124 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8235 (mt) REVERT: R 338 LEU cc_start: 0.8766 (tp) cc_final: 0.8524 (tp) outliers start: 10 outliers final: 6 residues processed: 112 average time/residue: 0.2159 time to fit residues: 31.3962 Evaluate side-chains 113 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 1 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 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 = 0.3533 r_free = 0.3533 target = 0.144749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.106849 restraints weight = 7862.207| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.09 r_work: 0.2943 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7122 Z= 0.129 Angle : 0.495 6.015 9676 Z= 0.262 Chirality : 0.041 0.148 1132 Planarity : 0.003 0.054 1170 Dihedral : 5.003 57.033 1274 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.30 % Favored : 96.58 % Rotamer: Outliers : 2.43 % Allowed : 12.30 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.30), residues: 848 helix: 2.16 (0.27), residues: 379 sheet: -0.68 (0.39), residues: 185 loop : -0.87 (0.36), residues: 284 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 0.013 0.001 PHE A 189 TYR 0.014 0.001 TYR R 182 ARG 0.006 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 392) hydrogen bonds : angle 4.36532 ( 1134) SS BOND : bond 0.00791 ( 2) SS BOND : angle 1.52326 ( 4) covalent geometry : bond 0.00300 ( 7120) covalent geometry : angle 0.49380 ( 9672) *********************** 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 129 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.758 Fit side-chains REVERT: A 255 ASN cc_start: 0.8611 (m110) cc_final: 0.8340 (m-40) REVERT: A 275 GLU cc_start: 0.8727 (tt0) cc_final: 0.8466 (tt0) REVERT: A 349 LYS cc_start: 0.8574 (ttpt) cc_final: 0.8073 (ttmt) REVERT: A 353 LEU cc_start: 0.8267 (mt) cc_final: 0.7992 (mt) REVERT: G 19 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7813 (tt) REVERT: R 124 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8067 (mp) REVERT: R 338 LEU cc_start: 0.8772 (tp) cc_final: 0.8471 (tp) outliers start: 18 outliers final: 12 residues processed: 120 average time/residue: 0.2001 time to fit residues: 31.7264 Evaluate side-chains 122 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 61 MET 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: 0.9980 chunk 68 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 0.0670 chunk 52 optimal weight: 0.7980 chunk 57 optimal weight: 0.0670 overall best weight: 0.4456 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.154911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.117941 restraints weight = 7541.009| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.03 r_work: 0.2962 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7122 Z= 0.112 Angle : 0.478 5.938 9676 Z= 0.255 Chirality : 0.040 0.143 1132 Planarity : 0.003 0.054 1170 Dihedral : 4.969 56.228 1274 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.83 % Favored : 97.05 % Rotamer: Outliers : 2.97 % Allowed : 12.70 % Favored : 84.32 % 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: 0.84 (0.30), residues: 848 helix: 2.20 (0.27), residues: 381 sheet: -0.69 (0.39), residues: 186 loop : -0.80 (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 0.014 0.001 TYR R 182 ARG 0.005 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03176 ( 392) hydrogen bonds : angle 4.30521 ( 1134) SS BOND : bond 0.00674 ( 2) SS BOND : angle 1.32534 ( 4) covalent geometry : bond 0.00255 ( 7120) covalent geometry : angle 0.47762 ( 9672) *********************** 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: 22 poor density : 113 time to evaluate : 0.778 Fit side-chains REVERT: A 275 GLU cc_start: 0.8706 (tt0) cc_final: 0.8452 (tt0) REVERT: A 349 LYS cc_start: 0.8613 (ttpt) cc_final: 0.8119 (ttmt) REVERT: A 353 LEU cc_start: 0.8256 (mt) cc_final: 0.7996 (mt) REVERT: B 20 ASP cc_start: 0.8055 (m-30) cc_final: 0.7711 (m-30) REVERT: G 19 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7826 (tt) REVERT: R 124 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8057 (mp) REVERT: R 212 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6275 (mp) REVERT: R 338 LEU cc_start: 0.8779 (tp) cc_final: 0.8439 (tp) outliers start: 22 outliers final: 13 residues processed: 125 average time/residue: 0.1993 time to fit residues: 32.8373 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 : 0.640 ------------------------------------------------------------------------------- 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: 7.9990 chunk 23 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.143241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.105162 restraints weight = 7819.774| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.09 r_work: 0.2922 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7122 Z= 0.149 Angle : 0.513 6.007 9676 Z= 0.272 Chirality : 0.042 0.148 1132 Planarity : 0.003 0.053 1170 Dihedral : 5.093 55.251 1274 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.30 % Favored : 96.58 % Rotamer: Outliers : 2.70 % Allowed : 14.32 % Favored : 82.97 % 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: 2.03 (0.27), residues: 387 sheet: -0.73 (0.39), residues: 177 loop : -0.88 (0.36), residues: 284 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 Details of bonding type rmsd hydrogen bonds : bond 0.03390 ( 392) hydrogen bonds : angle 4.36441 ( 1134) SS BOND : bond 0.00880 ( 2) SS BOND : angle 1.70635 ( 4) covalent geometry : bond 0.00352 ( 7120) covalent geometry : angle 0.51240 ( 9672) *********************** 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 133 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.777 Fit side-chains REVERT: A 275 GLU cc_start: 0.8747 (tt0) cc_final: 0.8320 (tt0) REVERT: A 349 LYS cc_start: 0.8641 (ttpt) cc_final: 0.8165 (ttmt) REVERT: B 20 ASP cc_start: 0.8029 (m-30) cc_final: 0.7699 (m-30) REVERT: G 19 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7769 (tt) REVERT: R 124 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8070 (mp) REVERT: R 212 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6326 (mp) outliers start: 20 outliers final: 13 residues processed: 123 average time/residue: 0.2055 time to fit residues: 33.0901 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 : 0.719 ------------------------------------------------------------------------------- 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 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 312 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: 0.7980 chunk 58 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3518 r_free = 0.3518 target = 0.143281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.104830 restraints weight = 7798.046| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.10 r_work: 0.2918 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1523 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= 0.150 Angle : 0.519 5.954 9676 Z= 0.272 Chirality : 0.041 0.143 1132 Planarity : 0.003 0.052 1170 Dihedral : 5.147 54.386 1274 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.95 % Favored : 96.93 % Rotamer: Outliers : 3.38 % Allowed : 14.19 % Favored : 82.43 % 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: 0.72 (0.30), residues: 848 helix: 2.08 (0.27), residues: 386 sheet: -0.78 (0.39), residues: 178 loop : -0.87 (0.36), residues: 284 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 0.006 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 392) hydrogen bonds : angle 4.37158 ( 1134) SS BOND : bond 0.00909 ( 2) SS BOND : angle 1.69068 ( 4) covalent geometry : bond 0.00357 ( 7120) covalent geometry : angle 0.51784 ( 9672) *********************** 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 133 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.782 Fit side-chains REVERT: A 229 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7726 (t0) REVERT: A 308 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8219 (mp0) REVERT: A 349 LYS cc_start: 0.8621 (ttpt) cc_final: 0.8148 (ttmt) REVERT: B 20 ASP cc_start: 0.8076 (m-30) cc_final: 0.7726 (m-30) REVERT: B 234 PHE cc_start: 0.9255 (OUTLIER) cc_final: 0.9021 (m-80) REVERT: G 19 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7701 (tt) REVERT: R 124 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8077 (mp) REVERT: R 212 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6306 (mp) REVERT: R 338 LEU cc_start: 0.8743 (tp) cc_final: 0.8381 (tp) outliers start: 25 outliers final: 14 residues processed: 121 average time/residue: 0.2072 time to fit residues: 33.0726 Evaluate side-chains 127 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 329 THR 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 188 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 38 optimal weight: 3.9990 chunk 65 optimal weight: 0.0980 chunk 2 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 55 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 chunk 21 optimal weight: 0.0050 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.3794 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.145575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.107611 restraints weight = 7795.542| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.09 r_work: 0.3013 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7122 Z= 0.108 Angle : 0.485 5.863 9676 Z= 0.258 Chirality : 0.040 0.137 1132 Planarity : 0.003 0.052 1170 Dihedral : 5.025 53.455 1274 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.18 % Favored : 96.70 % Rotamer: Outliers : 2.84 % Allowed : 15.00 % Favored : 82.16 % 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: 0.80 (0.30), residues: 848 helix: 2.13 (0.27), residues: 389 sheet: -0.78 (0.39), residues: 186 loop : -0.80 (0.36), 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 197 Details of bonding type rmsd hydrogen bonds : bond 0.03116 ( 392) hydrogen bonds : angle 4.27539 ( 1134) SS BOND : bond 0.00615 ( 2) SS BOND : angle 1.20922 ( 4) covalent geometry : bond 0.00246 ( 7120) covalent geometry : angle 0.48495 ( 9672) *********************** 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 134 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.723 Fit side-chains REVERT: A 229 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7727 (t0) REVERT: A 275 GLU cc_start: 0.8762 (tt0) cc_final: 0.8336 (tt0) REVERT: A 349 LYS cc_start: 0.8646 (ttpt) cc_final: 0.8216 (ttmt) REVERT: B 20 ASP cc_start: 0.8080 (m-30) cc_final: 0.7719 (m-30) REVERT: B 234 PHE cc_start: 0.9205 (OUTLIER) cc_final: 0.8842 (m-80) REVERT: G 19 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7765 (tt) REVERT: R 124 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8133 (mp) REVERT: R 212 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6391 (tt) REVERT: R 338 LEU cc_start: 0.8815 (tp) cc_final: 0.8465 (tp) outliers start: 21 outliers final: 11 residues processed: 126 average time/residue: 0.1964 time to fit residues: 32.7314 Evaluate side-chains 125 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 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 188 MET 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: 2.9990 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: 0.0980 chunk 22 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.141760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.102829 restraints weight = 7901.939| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.12 r_work: 0.2930 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7122 Z= 0.206 Angle : 0.578 6.080 9676 Z= 0.301 Chirality : 0.044 0.150 1132 Planarity : 0.004 0.053 1170 Dihedral : 5.349 51.881 1274 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.18 % Favored : 96.70 % Rotamer: Outliers : 2.70 % Allowed : 15.95 % 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: 0.64 (0.30), residues: 848 helix: 1.98 (0.27), residues: 387 sheet: -0.80 (0.39), residues: 179 loop : -0.88 (0.35), 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 0.017 0.002 PHE A 189 TYR 0.014 0.002 TYR R 182 ARG 0.006 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03725 ( 392) hydrogen bonds : angle 4.52248 ( 1134) SS BOND : bond 0.01139 ( 2) SS BOND : angle 2.18093 ( 4) covalent geometry : bond 0.00500 ( 7120) covalent geometry : angle 0.57593 ( 9672) *********************** 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 134 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.713 Fit side-chains REVERT: A 229 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7861 (t0) REVERT: A 275 GLU cc_start: 0.8817 (tt0) cc_final: 0.8380 (tt0) REVERT: A 349 LYS cc_start: 0.8733 (ttpt) cc_final: 0.8277 (ttmt) REVERT: B 20 ASP cc_start: 0.8158 (m-30) cc_final: 0.7791 (m-30) REVERT: G 19 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7774 (tt) REVERT: R 124 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8160 (mp) REVERT: R 212 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6399 (tt) REVERT: R 338 LEU cc_start: 0.8815 (tp) cc_final: 0.8432 (tp) outliers start: 20 outliers final: 11 residues processed: 123 average time/residue: 0.2023 time to fit residues: 32.8446 Evaluate side-chains 126 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 52 optimal weight: 0.2980 chunk 40 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 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 = 0.3519 r_free = 0.3519 target = 0.143153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.104361 restraints weight = 7825.267| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.11 r_work: 0.2922 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7122 Z= 0.145 Angle : 0.543 6.508 9676 Z= 0.284 Chirality : 0.042 0.143 1132 Planarity : 0.003 0.052 1170 Dihedral : 5.271 50.324 1274 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.18 % Favored : 96.70 % Rotamer: Outliers : 2.03 % Allowed : 17.16 % 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 (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: 2.11 (0.27), residues: 386 sheet: -0.78 (0.40), residues: 177 loop : -0.83 (0.35), residues: 285 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 0.014 0.001 PHE A 189 TYR 0.014 0.001 TYR R 182 ARG 0.006 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 392) hydrogen bonds : angle 4.42703 ( 1134) SS BOND : bond 0.00890 ( 2) SS BOND : angle 1.64657 ( 4) covalent geometry : bond 0.00344 ( 7120) covalent geometry : angle 0.54219 ( 9672) ********************** 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 126 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.759 Fit side-chains REVERT: A 229 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7750 (t0) REVERT: A 275 GLU cc_start: 0.8814 (tt0) cc_final: 0.8358 (tt0) REVERT: A 349 LYS cc_start: 0.8640 (ttpt) cc_final: 0.8225 (ttmt) REVERT: G 19 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7792 (tt) REVERT: R 124 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8108 (mp) REVERT: R 212 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6371 (tt) REVERT: R 338 LEU cc_start: 0.8805 (tp) cc_final: 0.8413 (tp) outliers start: 15 outliers final: 11 residues processed: 118 average time/residue: 0.2117 time to fit residues: 33.0646 Evaluate side-chains 126 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 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 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 43 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 59 optimal weight: 0.0870 chunk 6 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 39 optimal weight: 0.3980 chunk 64 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.144733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.106458 restraints weight = 7713.301| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.08 r_work: 0.2957 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7122 Z= 0.118 Angle : 0.517 6.331 9676 Z= 0.272 Chirality : 0.041 0.138 1132 Planarity : 0.003 0.052 1170 Dihedral : 5.120 49.342 1274 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.07 % Favored : 96.82 % Rotamer: Outliers : 2.03 % Allowed : 17.30 % Favored : 80.68 % 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: 0.85 (0.30), residues: 848 helix: 2.20 (0.27), residues: 386 sheet: -0.77 (0.39), residues: 185 loop : -0.77 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS R 112 PHE 0.011 0.001 PHE A 189 TYR 0.013 0.001 TYR R 182 ARG 0.006 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03185 ( 392) hydrogen bonds : angle 4.32355 ( 1134) SS BOND : bond 0.00707 ( 2) SS BOND : angle 1.34669 ( 4) covalent geometry : bond 0.00273 ( 7120) covalent geometry : angle 0.51650 ( 9672) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4038.35 seconds wall clock time: 70 minutes 49.51 seconds (4249.51 seconds total)