Starting phenix.real_space_refine on Sat Aug 3 04:55:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugy_42241/08_2024/8ugy_42241.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugy_42241/08_2024/8ugy_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugy_42241/08_2024/8ugy_42241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugy_42241/08_2024/8ugy_42241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugy_42241/08_2024/8ugy_42241.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugy_42241/08_2024/8ugy_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 Residue "A ASP 231": "OD1" <-> "OD2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 4.89, 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 - 3.50 Amino acid : False - 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: 2.94 Conformation dependent library (CDL) restraints added in 1.2 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: 0.78 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: 1.92 Time building geometry restraints manager: 3.16 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: 97.40 - 104.73: 93 104.73 - 112.06: 3688 112.06 - 119.38: 2383 119.38 - 126.71: 3405 126.71 - 134.04: 103 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: 1.470 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.130 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.610 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.683 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: 0.2335 time to fit residues: 37.6450 Evaluate side-chains 109 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 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 fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 0.710 Fit side-chains REVERT: A 349 LYS cc_start: 0.8492 (ttpt) cc_final: 0.7942 (ttmt) REVERT: R 124 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.7990 (mp) outliers start: 8 outliers final: 5 residues processed: 117 average time/residue: 0.2085 time to fit residues: 31.8310 Evaluate side-chains 116 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 42 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 62 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7120 Z= 0.190 Angle : 0.498 6.052 9672 Z= 0.265 Chirality : 0.041 0.152 1132 Planarity : 0.003 0.055 1170 Dihedral : 4.940 57.985 1274 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.59 % Favored : 97.29 % Rotamer: Outliers : 1.35 % Allowed : 11.22 % Favored : 87.43 % 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: 0.74 (0.30), residues: 848 helix: 2.12 (0.27), residues: 379 sheet: -0.69 (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 0.014 0.001 TYR R 182 ARG 0.003 0.000 ARG B 219 *********************** 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 fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.784 Fit side-chains REVERT: A 349 LYS cc_start: 0.8535 (ttpt) cc_final: 0.7956 (ttmt) REVERT: A 353 LEU cc_start: 0.8205 (mt) cc_final: 0.7955 (mt) REVERT: R 124 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8047 (mt) REVERT: R 338 LEU cc_start: 0.8800 (tp) cc_final: 0.8548 (tp) outliers start: 10 outliers final: 7 residues processed: 112 average time/residue: 0.2211 time to fit residues: 32.1808 Evaluate side-chains 113 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 76 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 73 optimal weight: 0.0040 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7120 Z= 0.184 Angle : 0.488 5.999 9672 Z= 0.260 Chirality : 0.041 0.148 1132 Planarity : 0.003 0.053 1170 Dihedral : 4.991 56.939 1274 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.30 % Favored : 96.58 % Rotamer: Outliers : 2.43 % Allowed : 12.16 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.30), residues: 848 helix: 2.18 (0.27), residues: 379 sheet: -0.66 (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 0.012 0.001 PHE A 189 TYR 0.014 0.001 TYR R 182 ARG 0.006 0.000 ARG B 197 *********************** 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 130 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 0.671 Fit side-chains REVERT: A 275 GLU cc_start: 0.8601 (tt0) cc_final: 0.8388 (tt0) REVERT: A 349 LYS cc_start: 0.8578 (ttpt) cc_final: 0.8013 (ttmt) REVERT: A 353 LEU cc_start: 0.8274 (mt) cc_final: 0.8035 (mt) REVERT: G 19 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7895 (tt) REVERT: R 124 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.7895 (mp) REVERT: R 338 LEU cc_start: 0.8799 (tp) cc_final: 0.8489 (tp) outliers start: 18 outliers final: 10 residues processed: 120 average time/residue: 0.2182 time to fit residues: 34.5330 Evaluate side-chains 121 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 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 46 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN R 40 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7120 Z= 0.349 Angle : 0.577 6.155 9672 Z= 0.303 Chirality : 0.044 0.157 1132 Planarity : 0.004 0.054 1170 Dihedral : 5.426 55.441 1274 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.30 % Favored : 96.58 % Rotamer: Outliers : 3.24 % Allowed : 12.84 % Favored : 83.92 % 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: 0.53 (0.30), residues: 848 helix: 1.88 (0.27), residues: 386 sheet: -0.84 (0.39), residues: 179 loop : -0.92 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.017 0.002 PHE R 300 TYR 0.013 0.002 TYR R 182 ARG 0.006 0.001 ARG B 19 *********************** 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 142 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 0.701 Fit side-chains REVERT: A 188 HIS cc_start: 0.7361 (t70) cc_final: 0.7070 (t70) REVERT: A 264 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8516 (mt) REVERT: A 349 LYS cc_start: 0.8599 (ttpt) cc_final: 0.8065 (ttmt) REVERT: B 20 ASP cc_start: 0.8082 (m-30) cc_final: 0.7793 (m-30) REVERT: B 198 LEU cc_start: 0.9125 (mp) cc_final: 0.8835 (mp) REVERT: G 19 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7887 (tt) REVERT: R 124 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.7952 (mp) REVERT: R 212 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.6653 (mp) outliers start: 24 outliers final: 13 residues processed: 131 average time/residue: 0.2068 time to fit residues: 35.6419 Evaluate side-chains 130 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ILE 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 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 100 SER Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 321 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1567 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= 0.219 Angle : 0.518 5.991 9672 Z= 0.273 Chirality : 0.041 0.142 1132 Planarity : 0.003 0.053 1170 Dihedral : 5.302 54.648 1274 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.42 % Favored : 96.46 % Rotamer: Outliers : 3.38 % Allowed : 14.32 % Favored : 82.30 % 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: 383 sheet: -0.79 (0.39), residues: 182 loop : -0.88 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 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 0.005 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 138 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 0.802 Fit side-chains REVERT: A 229 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7550 (t0) REVERT: A 275 GLU cc_start: 0.8625 (tt0) cc_final: 0.8250 (tt0) REVERT: A 349 LYS cc_start: 0.8589 (ttpt) cc_final: 0.8050 (ttmt) REVERT: B 234 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.8992 (m-80) REVERT: G 19 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7840 (tt) REVERT: R 124 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.7907 (mp) REVERT: R 212 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6561 (mp) REVERT: R 338 LEU cc_start: 0.8799 (tp) cc_final: 0.8394 (tp) outliers start: 25 outliers final: 16 residues processed: 125 average time/residue: 0.2161 time to fit residues: 35.8175 Evaluate side-chains 133 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 45 MET Chi-restraints excluded: chain R residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1658 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= 0.235 Angle : 0.525 5.967 9672 Z= 0.276 Chirality : 0.042 0.143 1132 Planarity : 0.003 0.052 1170 Dihedral : 5.310 54.029 1274 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.18 % Favored : 96.70 % Rotamer: Outliers : 3.51 % Allowed : 15.41 % Favored : 81.08 % 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: 384 sheet: -0.78 (0.40), residues: 177 loop : -0.90 (0.35), residues: 287 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 0.014 0.001 PHE R 300 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 137 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 0.751 Fit side-chains REVERT: A 275 GLU cc_start: 0.8632 (tt0) cc_final: 0.8257 (tt0) REVERT: A 308 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8140 (mp0) REVERT: A 349 LYS cc_start: 0.8580 (ttpt) cc_final: 0.8040 (ttmt) REVERT: B 20 ASP cc_start: 0.8143 (m-30) cc_final: 0.7828 (m-30) REVERT: B 234 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.8998 (m-80) REVERT: G 19 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7839 (tt) REVERT: R 124 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.7918 (mp) REVERT: R 212 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6581 (mp) REVERT: R 338 LEU cc_start: 0.8805 (tp) cc_final: 0.8360 (tp) outliers start: 26 outliers final: 14 residues processed: 123 average time/residue: 0.2035 time to fit residues: 32.9842 Evaluate side-chains 130 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 48 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7120 Z= 0.347 Angle : 0.588 7.857 9672 Z= 0.306 Chirality : 0.044 0.149 1132 Planarity : 0.004 0.053 1170 Dihedral : 5.595 52.131 1274 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.42 % Favored : 96.46 % Rotamer: Outliers : 3.24 % Allowed : 16.08 % 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: 0.56 (0.30), residues: 848 helix: 1.95 (0.27), residues: 383 sheet: -0.86 (0.40), residues: 179 loop : -0.92 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.017 0.002 PHE A 189 TYR 0.014 0.002 TYR R 182 ARG 0.006 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 142 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 0.716 Fit side-chains REVERT: A 308 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8033 (mp0) REVERT: A 349 LYS cc_start: 0.8524 (ttpt) cc_final: 0.7972 (ttmt) REVERT: G 19 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7811 (tt) REVERT: R 124 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.7949 (mp) REVERT: R 212 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6693 (mp) REVERT: R 338 LEU cc_start: 0.8836 (tp) cc_final: 0.8436 (tp) outliers start: 24 outliers final: 14 residues processed: 130 average time/residue: 0.2030 time to fit residues: 34.7345 Evaluate side-chains 137 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 312 LEU Chi-restraints excluded: chain R residue 321 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7120 Z= 0.234 Angle : 0.545 7.100 9672 Z= 0.285 Chirality : 0.042 0.142 1132 Planarity : 0.004 0.052 1170 Dihedral : 5.465 51.094 1274 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.07 % Favored : 96.82 % Rotamer: Outliers : 2.84 % Allowed : 17.30 % Favored : 79.86 % 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: 0.68 (0.30), residues: 848 helix: 2.08 (0.27), residues: 382 sheet: -0.82 (0.40), residues: 179 loop : -0.88 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.013 0.001 PHE R 300 TYR 0.014 0.001 TYR R 182 ARG 0.006 0.000 ARG B 197 *********************** 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 fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 0.775 Fit side-chains REVERT: A 275 GLU cc_start: 0.8644 (tt0) cc_final: 0.8257 (tt0) REVERT: A 308 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8137 (mp0) REVERT: A 349 LYS cc_start: 0.8585 (ttpt) cc_final: 0.8037 (ttmt) REVERT: G 19 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7770 (tt) REVERT: R 124 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.7919 (mp) REVERT: R 212 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6605 (mp) REVERT: R 338 LEU cc_start: 0.8825 (tp) cc_final: 0.8404 (tp) outliers start: 21 outliers final: 15 residues processed: 125 average time/residue: 0.2066 time to fit residues: 33.8608 Evaluate side-chains 131 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 100 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 189 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7120 Z= 0.244 Angle : 0.547 7.272 9672 Z= 0.286 Chirality : 0.042 0.143 1132 Planarity : 0.003 0.053 1170 Dihedral : 5.433 50.471 1274 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.30 % Favored : 96.58 % Rotamer: Outliers : 3.11 % Allowed : 16.76 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.15 (0.27), residues: 378 sheet: -0.81 (0.40), residues: 179 loop : -0.83 (0.35), residues: 291 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 0.014 0.001 PHE A 189 TYR 0.014 0.001 TYR R 182 ARG 0.006 0.000 ARG B 197 ********************** 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 138 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 0.816 Fit side-chains REVERT: A 275 GLU cc_start: 0.8648 (tt0) cc_final: 0.8259 (tt0) REVERT: A 308 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8152 (mp0) REVERT: A 349 LYS cc_start: 0.8587 (ttpt) cc_final: 0.8039 (ttmt) REVERT: G 19 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7785 (tt) REVERT: R 124 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.7927 (mp) REVERT: R 212 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6603 (mp) REVERT: R 338 LEU cc_start: 0.8823 (tp) cc_final: 0.8362 (tp) outliers start: 23 outliers final: 18 residues processed: 127 average time/residue: 0.2002 time to fit residues: 33.4095 Evaluate side-chains 135 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 100 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 189 SER 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 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 20 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 59 optimal weight: 0.0980 chunk 3 optimal weight: 0.5980 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 = 0.3514 r_free = 0.3514 target = 0.142668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.104881 restraints weight = 7690.338| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.08 r_work: 0.2924 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7120 Z= 0.205 Angle : 0.530 6.735 9672 Z= 0.277 Chirality : 0.041 0.139 1132 Planarity : 0.003 0.053 1170 Dihedral : 5.344 50.260 1274 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.30 % Favored : 96.58 % Rotamer: Outliers : 2.84 % Allowed : 17.16 % Favored : 80.00 % 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: 2.17 (0.27), residues: 381 sheet: -0.80 (0.41), residues: 178 loop : -0.74 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.012 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: 1863.19 seconds wall clock time: 34 minutes 3.71 seconds (2043.71 seconds total)