Starting phenix.real_space_refine on Thu Nov 14 20:01:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4p_36889/11_2024/8k4p_36889.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4p_36889/11_2024/8k4p_36889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4p_36889/11_2024/8k4p_36889.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4p_36889/11_2024/8k4p_36889.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4p_36889/11_2024/8k4p_36889.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4p_36889/11_2024/8k4p_36889.cif" } resolution = 2.81 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= -0.001 sd= 0.047 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 54 5.16 5 C 4600 2.51 5 N 1250 2.21 5 O 1327 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7231 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "A" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2345 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 6, 'TRANS': 287} Chain: "C" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1867 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 229} Chain breaks: 1 Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Time building chain proxies: 4.88, per 1000 atoms: 0.67 Number of scatterers: 7231 At special positions: 0 Unit cell: (78.2, 102.85, 136.85, 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 54 16.00 O 1327 8.00 N 1250 7.00 C 4600 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 196 " distance=2.04 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: 1.62 Conformation dependent library (CDL) restraints added in 1.6 seconds 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 8 sheets defined 44.3% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'A' and resid 48 through 75 removed outlier: 3.633A pdb=" N LEU A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 91 removed outlier: 3.657A pdb=" N ILE A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 removed outlier: 3.693A pdb=" N LEU A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 149 removed outlier: 4.024A pdb=" N CYS A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG A 119 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP A 132 " --> pdb=" O TYR A 128 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A 133 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 183 removed outlier: 4.305A pdb=" N GLY A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 169 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 181 " --> pdb=" O GLY A 177 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 220 Processing helix chain 'A' and resid 221 through 239 removed outlier: 3.626A pdb=" N VAL A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 279 removed outlier: 3.815A pdb=" N GLY A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Proline residue: A 266 - end of helix Processing helix chain 'A' and resid 287 through 318 removed outlier: 3.789A pdb=" N LEU A 291 " --> pdb=" O TYR A 287 " (cutoff:3.500A) Proline residue: A 311 - end of helix removed outlier: 4.025A pdb=" N GLY A 318 " --> pdb=" O TYR A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 336 removed outlier: 3.520A pdb=" N ARG A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 31 removed outlier: 3.659A pdb=" N ALA C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 53 Processing helix chain 'C' and resid 207 through 216 removed outlier: 3.529A pdb=" N LYS C 210 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 216 " --> pdb=" O HIS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 255 removed outlier: 3.739A pdb=" N GLU C 245 " --> pdb=" O ASN C 241 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER C 246 " --> pdb=" O ARG C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 275 Processing helix chain 'C' and resid 276 through 281 Processing helix chain 'C' and resid 295 through 309 removed outlier: 4.195A pdb=" N TYR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE C 303 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS C 305 " --> pdb=" O ALA C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 351 removed outlier: 3.875A pdb=" N ASP C 341 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE C 344 " --> pdb=" O THR C 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.512A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.862A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.656A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.871A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.658A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.136A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.551A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.961A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.647A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.790A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 184 through 190 removed outlier: 6.249A pdb=" N VAL C 34 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N PHE C 199 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N VAL C 201 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU C 38 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 1020 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: 2.01 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1363 1.33 - 1.45: 1837 1.45 - 1.58: 4093 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 7367 Sorted by residual: bond pdb=" CA ARG C 24 " pdb=" C ARG C 24 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.37e-02 5.33e+03 9.33e+00 bond pdb=" CA MET C 18 " pdb=" CB MET C 18 " ideal model delta sigma weight residual 1.528 1.482 0.046 1.66e-02 3.63e+03 7.70e+00 bond pdb=" CA LYS C 280 " pdb=" C LYS C 280 " ideal model delta sigma weight residual 1.524 1.506 0.018 7.00e-03 2.04e+04 6.89e+00 bond pdb=" C MET C 18 " pdb=" O MET C 18 " ideal model delta sigma weight residual 1.236 1.203 0.033 1.26e-02 6.30e+03 6.81e+00 bond pdb=" C ARG C 24 " pdb=" O ARG C 24 " ideal model delta sigma weight residual 1.236 1.203 0.034 1.29e-02 6.01e+03 6.77e+00 ... (remaining 7362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 9736 1.61 - 3.23: 189 3.23 - 4.84: 33 4.84 - 6.46: 7 6.46 - 8.07: 4 Bond angle restraints: 9969 Sorted by residual: angle pdb=" N ARG A 185 " pdb=" CA ARG A 185 " pdb=" C ARG A 185 " ideal model delta sigma weight residual 110.43 103.69 6.74 1.31e+00 5.83e-01 2.65e+01 angle pdb=" C SER A 285 " pdb=" N CYS A 286 " pdb=" CA CYS A 286 " ideal model delta sigma weight residual 121.54 128.44 -6.90 1.91e+00 2.74e-01 1.31e+01 angle pdb=" C LYS C 280 " pdb=" CA LYS C 280 " pdb=" CB LYS C 280 " ideal model delta sigma weight residual 111.65 106.72 4.93 1.44e+00 4.82e-01 1.17e+01 angle pdb=" O LEU C 23 " pdb=" C LEU C 23 " pdb=" N ARG C 24 " ideal model delta sigma weight residual 122.12 118.92 3.20 1.06e+00 8.90e-01 9.13e+00 angle pdb=" CA ILE A 282 " pdb=" CB ILE A 282 " pdb=" CG1 ILE A 282 " ideal model delta sigma weight residual 110.40 115.28 -4.88 1.70e+00 3.46e-01 8.23e+00 ... (remaining 9964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 3707 17.13 - 34.26: 504 34.26 - 51.38: 140 51.38 - 68.51: 32 68.51 - 85.64: 12 Dihedral angle restraints: 4395 sinusoidal: 1724 harmonic: 2671 Sorted by residual: dihedral pdb=" CA LEU C 268 " pdb=" C LEU C 268 " pdb=" N ASN C 269 " pdb=" CA ASN C 269 " ideal model delta harmonic sigma weight residual -180.00 -157.83 -22.17 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA MET A 195 " pdb=" C MET A 195 " pdb=" N CYS A 196 " pdb=" CA CYS A 196 " ideal model delta harmonic sigma weight residual 180.00 160.43 19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA ILE A 112 " pdb=" C ILE A 112 " pdb=" N ILE A 113 " pdb=" CA ILE A 113 " ideal model delta harmonic sigma weight residual -180.00 -160.65 -19.35 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 4392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 801 0.038 - 0.076: 262 0.076 - 0.114: 70 0.114 - 0.151: 15 0.151 - 0.189: 1 Chirality restraints: 1149 Sorted by residual: chirality pdb=" CA VAL A 310 " pdb=" N VAL A 310 " pdb=" C VAL A 310 " pdb=" CB VAL A 310 " both_signs ideal model delta sigma weight residual False 2.44 2.25 0.19 2.00e-01 2.50e+01 8.96e-01 chirality pdb=" CA TRP A 154 " pdb=" N TRP A 154 " pdb=" C TRP A 154 " pdb=" CB TRP A 154 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ILE C 265 " pdb=" N ILE C 265 " pdb=" C ILE C 265 " pdb=" CB ILE C 265 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 1146 not shown) Planarity restraints: 1255 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 310 " 0.041 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO A 311 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 311 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 311 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO B 236 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 242 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.66e+00 pdb=" C LYS A 242 " 0.028 2.00e-02 2.50e+03 pdb=" O LYS A 242 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 243 " -0.010 2.00e-02 2.50e+03 ... (remaining 1252 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 124 2.68 - 3.23: 6676 3.23 - 3.79: 10460 3.79 - 4.34: 14814 4.34 - 4.90: 24949 Nonbonded interactions: 57023 Sorted by model distance: nonbonded pdb=" OG SER A 99 " pdb=" OE2 GLU A 121 " model vdw 2.120 3.040 nonbonded pdb=" OD1 ASN A 61 " pdb=" OG SER A 93 " model vdw 2.145 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.209 3.040 nonbonded pdb=" O ALA A 172 " pdb=" OG SER A 176 " model vdw 2.235 3.040 nonbonded pdb=" NH1 ARG A 183 " pdb=" O CYS A 196 " model vdw 2.246 3.120 ... (remaining 57018 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: 1.530 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: 19.760 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 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 0.046 7367 Z= 0.198 Angle : 0.579 8.070 9969 Z= 0.325 Chirality : 0.041 0.189 1149 Planarity : 0.004 0.061 1255 Dihedral : 17.491 85.640 2664 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.53 % Allowed : 27.88 % Favored : 69.58 % 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: 0.06 (0.27), residues: 908 helix: 1.07 (0.27), residues: 369 sheet: 1.15 (0.38), residues: 174 loop : -1.66 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS A 210 PHE 0.013 0.001 PHE A 329 TYR 0.010 0.001 TYR A 128 ARG 0.006 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 203 MET cc_start: 0.4125 (ttt) cc_final: 0.3760 (ppp) REVERT: C 18 MET cc_start: 0.7522 (ttp) cc_final: 0.7259 (ttp) REVERT: C 24 ARG cc_start: 0.7550 (ptm160) cc_final: 0.7175 (ptp90) REVERT: C 29 LYS cc_start: 0.7801 (ttmt) cc_final: 0.7482 (tttm) outliers start: 20 outliers final: 17 residues processed: 106 average time/residue: 1.3892 time to fit residues: 154.9396 Evaluate side-chains 101 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 332 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 46 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7367 Z= 0.196 Angle : 0.529 6.730 9969 Z= 0.283 Chirality : 0.041 0.165 1149 Planarity : 0.004 0.045 1255 Dihedral : 5.795 58.049 1023 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 6.08 % Allowed : 22.56 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.27), residues: 908 helix: 1.65 (0.27), residues: 384 sheet: 1.20 (0.39), residues: 171 loop : -1.88 (0.27), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 182 PHE 0.015 0.001 PHE A 134 TYR 0.010 0.001 TYR A 128 ARG 0.005 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 89 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: B 16 ASN cc_start: 0.7827 (OUTLIER) cc_final: 0.7610 (m-40) REVERT: B 226 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7583 (mm-30) REVERT: B 258 ASP cc_start: 0.8277 (t0) cc_final: 0.8039 (t0) REVERT: A 106 MET cc_start: 0.6603 (tpt) cc_final: 0.6227 (tmm) REVERT: A 175 LEU cc_start: 0.7640 (mt) cc_final: 0.7432 (mt) REVERT: A 190 VAL cc_start: 0.2301 (OUTLIER) cc_final: 0.1960 (t) REVERT: A 203 MET cc_start: 0.4316 (ttt) cc_final: 0.3930 (ppp) REVERT: A 212 ARG cc_start: 0.6883 (mmm-85) cc_final: 0.6673 (mmm-85) REVERT: A 273 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7231 (tt) REVERT: C 20 ASP cc_start: 0.8111 (t0) cc_final: 0.7419 (m-30) REVERT: C 24 ARG cc_start: 0.7210 (ptm160) cc_final: 0.6918 (ptp90) REVERT: C 233 VAL cc_start: 0.7953 (OUTLIER) cc_final: 0.7624 (p) REVERT: C 240 MET cc_start: 0.5348 (OUTLIER) cc_final: 0.5113 (ttt) outliers start: 48 outliers final: 16 residues processed: 124 average time/residue: 1.1855 time to fit residues: 155.6612 Evaluate side-chains 104 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 327 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 GLN ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7367 Z= 0.199 Angle : 0.514 6.602 9969 Z= 0.275 Chirality : 0.041 0.181 1149 Planarity : 0.003 0.043 1255 Dihedral : 5.464 59.104 1010 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 5.96 % Allowed : 22.31 % Favored : 71.74 % 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: 0.58 (0.28), residues: 908 helix: 1.97 (0.28), residues: 385 sheet: 1.18 (0.39), residues: 166 loop : -1.91 (0.27), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 182 PHE 0.015 0.001 PHE A 72 TYR 0.010 0.001 TYR A 128 ARG 0.003 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 83 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: B 44 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7944 (mt0) REVERT: B 226 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7557 (mm-30) REVERT: A 106 MET cc_start: 0.6700 (tpt) cc_final: 0.6196 (tmm) REVERT: A 190 VAL cc_start: 0.1995 (OUTLIER) cc_final: 0.1656 (t) REVERT: A 203 MET cc_start: 0.4521 (ttt) cc_final: 0.3977 (ppp) REVERT: A 273 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7258 (tt) REVERT: C 20 ASP cc_start: 0.8117 (t0) cc_final: 0.7433 (m-30) REVERT: C 24 ARG cc_start: 0.7149 (ptm160) cc_final: 0.6858 (ptp90) REVERT: C 233 VAL cc_start: 0.7961 (OUTLIER) cc_final: 0.7628 (p) REVERT: C 279 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7388 (mptt) outliers start: 47 outliers final: 20 residues processed: 116 average time/residue: 1.2486 time to fit residues: 152.7232 Evaluate side-chains 108 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 9.9990 chunk 42 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.2980 chunk 54 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 0.0980 chunk 23 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7367 Z= 0.143 Angle : 0.474 6.676 9969 Z= 0.253 Chirality : 0.039 0.160 1149 Planarity : 0.003 0.042 1255 Dihedral : 5.024 59.224 1008 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.69 % Allowed : 23.70 % Favored : 71.61 % 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 (0.28), residues: 908 helix: 2.18 (0.28), residues: 385 sheet: 1.26 (0.38), residues: 167 loop : -1.87 (0.27), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS A 182 PHE 0.018 0.001 PHE A 134 TYR 0.008 0.001 TYR B 124 ARG 0.003 0.000 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 83 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8160 (mp) cc_final: 0.7939 (mp) REVERT: A 106 MET cc_start: 0.6715 (tpt) cc_final: 0.6234 (tmm) REVERT: A 183 ARG cc_start: 0.5068 (ttm-80) cc_final: 0.4488 (ttm170) REVERT: A 190 VAL cc_start: 0.1885 (OUTLIER) cc_final: 0.1584 (t) REVERT: A 203 MET cc_start: 0.4344 (ttt) cc_final: 0.3978 (ppp) REVERT: A 333 ARG cc_start: 0.6467 (OUTLIER) cc_final: 0.5128 (tpt170) REVERT: C 20 ASP cc_start: 0.8070 (t0) cc_final: 0.7391 (m-30) REVERT: C 24 ARG cc_start: 0.7065 (ptm160) cc_final: 0.6807 (ptp90) REVERT: C 184 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8376 (tp) REVERT: C 233 VAL cc_start: 0.7956 (OUTLIER) cc_final: 0.7618 (p) REVERT: C 279 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7485 (mtpt) outliers start: 37 outliers final: 14 residues processed: 112 average time/residue: 1.2428 time to fit residues: 146.9831 Evaluate side-chains 99 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7367 Z= 0.223 Angle : 0.512 6.494 9969 Z= 0.273 Chirality : 0.041 0.171 1149 Planarity : 0.003 0.041 1255 Dihedral : 5.040 55.454 1007 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 5.96 % Allowed : 22.18 % Favored : 71.86 % 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: 0.69 (0.28), residues: 908 helix: 2.15 (0.28), residues: 386 sheet: 1.17 (0.39), residues: 166 loop : -1.94 (0.27), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 182 PHE 0.017 0.001 PHE A 134 TYR 0.012 0.001 TYR A 128 ARG 0.002 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 79 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: B 44 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8007 (mt0) REVERT: B 258 ASP cc_start: 0.8277 (t0) cc_final: 0.8031 (t0) REVERT: B 336 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8467 (mt) REVERT: A 106 MET cc_start: 0.6765 (tpt) cc_final: 0.6266 (tmm) REVERT: A 183 ARG cc_start: 0.5258 (ttm-80) cc_final: 0.4807 (ttm170) REVERT: A 190 VAL cc_start: 0.1705 (OUTLIER) cc_final: 0.1440 (t) REVERT: A 203 MET cc_start: 0.4348 (ttt) cc_final: 0.3795 (ppp) REVERT: A 273 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7480 (tt) REVERT: A 333 ARG cc_start: 0.6511 (OUTLIER) cc_final: 0.6086 (tmm160) REVERT: C 20 ASP cc_start: 0.8125 (t0) cc_final: 0.7434 (m-30) REVERT: C 24 ARG cc_start: 0.7168 (ptm160) cc_final: 0.6871 (ptp90) REVERT: C 233 VAL cc_start: 0.7951 (OUTLIER) cc_final: 0.7629 (p) REVERT: C 279 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7476 (mtpt) outliers start: 47 outliers final: 24 residues processed: 113 average time/residue: 0.9428 time to fit residues: 112.9377 Evaluate side-chains 110 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 79 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.8454 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7367 Z= 0.341 Angle : 0.580 7.919 9969 Z= 0.308 Chirality : 0.043 0.185 1149 Planarity : 0.004 0.043 1255 Dihedral : 5.287 54.643 1007 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 6.59 % Allowed : 21.42 % Favored : 71.99 % 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: 0.45 (0.28), residues: 908 helix: 1.88 (0.28), residues: 384 sheet: 1.08 (0.39), residues: 166 loop : -1.97 (0.27), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 182 PHE 0.018 0.002 PHE A 124 TYR 0.015 0.001 TYR A 128 ARG 0.002 0.000 ARG A 119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 81 time to evaluate : 0.866 Fit side-chains REVERT: B 258 ASP cc_start: 0.8346 (t0) cc_final: 0.8075 (t0) REVERT: B 301 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.6869 (mtpt) REVERT: B 336 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8538 (mt) REVERT: A 106 MET cc_start: 0.6664 (tpt) cc_final: 0.6186 (tmm) REVERT: A 183 ARG cc_start: 0.5302 (ttm-80) cc_final: 0.4836 (ttm170) REVERT: A 190 VAL cc_start: 0.1658 (OUTLIER) cc_final: 0.1414 (t) REVERT: A 203 MET cc_start: 0.4163 (ttt) cc_final: 0.3705 (ppp) REVERT: A 273 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7498 (tt) REVERT: A 333 ARG cc_start: 0.6628 (OUTLIER) cc_final: 0.6090 (tmm160) REVERT: C 24 ARG cc_start: 0.7298 (ptm160) cc_final: 0.6975 (ptp90) REVERT: C 233 VAL cc_start: 0.7947 (OUTLIER) cc_final: 0.7608 (p) outliers start: 52 outliers final: 21 residues processed: 120 average time/residue: 1.3370 time to fit residues: 168.6619 Evaluate side-chains 108 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7367 Z= 0.197 Angle : 0.506 6.873 9969 Z= 0.269 Chirality : 0.040 0.169 1149 Planarity : 0.004 0.041 1255 Dihedral : 4.598 46.454 1003 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.69 % Allowed : 23.32 % Favored : 71.99 % 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: 0.63 (0.28), residues: 908 helix: 2.08 (0.28), residues: 384 sheet: 1.17 (0.39), residues: 165 loop : -1.94 (0.27), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS A 182 PHE 0.015 0.001 PHE A 134 TYR 0.011 0.001 TYR A 128 ARG 0.005 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 80 time to evaluate : 0.843 Fit side-chains REVERT: B 258 ASP cc_start: 0.8326 (t0) cc_final: 0.8117 (t0) REVERT: B 325 MET cc_start: 0.8871 (mmt) cc_final: 0.8416 (mmt) REVERT: B 336 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8507 (mt) REVERT: A 106 MET cc_start: 0.6608 (tpt) cc_final: 0.6192 (tmm) REVERT: A 183 ARG cc_start: 0.5294 (ttm-80) cc_final: 0.4803 (ttm170) REVERT: A 190 VAL cc_start: 0.1582 (OUTLIER) cc_final: 0.1346 (t) REVERT: A 203 MET cc_start: 0.4449 (ttt) cc_final: 0.3848 (ppp) REVERT: A 333 ARG cc_start: 0.6604 (OUTLIER) cc_final: 0.5289 (tpt170) REVERT: C 24 ARG cc_start: 0.7150 (ptm160) cc_final: 0.6884 (ptp90) REVERT: C 233 VAL cc_start: 0.7941 (OUTLIER) cc_final: 0.7597 (p) REVERT: C 249 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8136 (tt) outliers start: 37 outliers final: 23 residues processed: 108 average time/residue: 1.2140 time to fit residues: 139.0120 Evaluate side-chains 106 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 59 optimal weight: 0.3980 chunk 42 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 78 optimal weight: 8.9990 chunk 83 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7367 Z= 0.142 Angle : 0.471 6.861 9969 Z= 0.251 Chirality : 0.039 0.158 1149 Planarity : 0.003 0.040 1255 Dihedral : 4.293 41.961 1003 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.30 % Allowed : 25.22 % Favored : 71.48 % 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 (0.28), residues: 908 helix: 2.33 (0.28), residues: 385 sheet: 1.13 (0.39), residues: 163 loop : -1.94 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS A 182 PHE 0.014 0.001 PHE A 134 TYR 0.008 0.001 TYR A 128 ARG 0.003 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.940 Fit side-chains REVERT: B 258 ASP cc_start: 0.8287 (t0) cc_final: 0.8049 (t0) REVERT: B 325 MET cc_start: 0.8850 (mmt) cc_final: 0.8368 (mmt) REVERT: A 106 MET cc_start: 0.6546 (tpt) cc_final: 0.6212 (tmm) REVERT: A 183 ARG cc_start: 0.5245 (ttm-80) cc_final: 0.4676 (ttm170) REVERT: A 190 VAL cc_start: 0.1710 (OUTLIER) cc_final: 0.1427 (t) REVERT: A 203 MET cc_start: 0.4483 (ttt) cc_final: 0.3791 (ppp) REVERT: A 273 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7534 (tt) REVERT: A 333 ARG cc_start: 0.6444 (OUTLIER) cc_final: 0.5213 (tpt170) REVERT: C 24 ARG cc_start: 0.7054 (ptm160) cc_final: 0.6794 (ptp90) REVERT: C 233 VAL cc_start: 0.7868 (OUTLIER) cc_final: 0.7519 (p) REVERT: C 249 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8178 (tt) outliers start: 26 outliers final: 17 residues processed: 103 average time/residue: 1.2849 time to fit residues: 140.1978 Evaluate side-chains 100 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 0.1980 chunk 76 optimal weight: 0.0970 chunk 53 optimal weight: 0.1980 chunk 85 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7367 Z= 0.145 Angle : 0.474 6.850 9969 Z= 0.251 Chirality : 0.039 0.171 1149 Planarity : 0.003 0.040 1255 Dihedral : 4.162 41.239 1003 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.93 % Allowed : 24.21 % Favored : 71.86 % 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: 0.85 (0.28), residues: 908 helix: 2.35 (0.28), residues: 386 sheet: 1.08 (0.38), residues: 169 loop : -1.88 (0.28), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 182 PHE 0.015 0.001 PHE A 134 TYR 0.008 0.001 TYR A 128 ARG 0.002 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 80 time to evaluate : 0.790 Fit side-chains REVERT: B 325 MET cc_start: 0.8842 (mmt) cc_final: 0.8358 (mmt) REVERT: A 106 MET cc_start: 0.6635 (tpt) cc_final: 0.6270 (tmm) REVERT: A 183 ARG cc_start: 0.5213 (ttm-80) cc_final: 0.4770 (ttm170) REVERT: A 190 VAL cc_start: 0.1721 (OUTLIER) cc_final: 0.1437 (t) REVERT: A 203 MET cc_start: 0.4594 (ttt) cc_final: 0.3908 (ppp) REVERT: A 333 ARG cc_start: 0.6459 (OUTLIER) cc_final: 0.5231 (tpt170) REVERT: C 24 ARG cc_start: 0.7065 (ptm160) cc_final: 0.6799 (ptp90) REVERT: C 233 VAL cc_start: 0.7954 (OUTLIER) cc_final: 0.7615 (p) REVERT: C 279 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7512 (mtpt) outliers start: 31 outliers final: 17 residues processed: 104 average time/residue: 1.2554 time to fit residues: 138.1626 Evaluate side-chains 98 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 89 optimal weight: 0.0020 chunk 82 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 21 optimal weight: 0.0980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7367 Z= 0.153 Angle : 0.480 8.684 9969 Z= 0.253 Chirality : 0.039 0.174 1149 Planarity : 0.003 0.039 1255 Dihedral : 4.123 40.743 1003 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.92 % Allowed : 25.73 % Favored : 71.36 % 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: 0.87 (0.28), residues: 908 helix: 2.38 (0.28), residues: 387 sheet: 1.10 (0.39), residues: 164 loop : -1.87 (0.28), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 182 PHE 0.014 0.001 PHE A 134 TYR 0.009 0.001 TYR A 128 ARG 0.002 0.000 ARG A 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.842 Fit side-chains REVERT: B 325 MET cc_start: 0.8841 (mmt) cc_final: 0.8394 (mmt) REVERT: A 106 MET cc_start: 0.6675 (tpt) cc_final: 0.6342 (tmm) REVERT: A 183 ARG cc_start: 0.5204 (ttm-80) cc_final: 0.4743 (ttm170) REVERT: A 190 VAL cc_start: 0.1637 (OUTLIER) cc_final: 0.1356 (t) REVERT: A 203 MET cc_start: 0.4449 (ttt) cc_final: 0.3813 (ppp) REVERT: A 333 ARG cc_start: 0.6457 (OUTLIER) cc_final: 0.5236 (tpt170) REVERT: C 24 ARG cc_start: 0.7058 (ptm160) cc_final: 0.6797 (ptp90) REVERT: C 233 VAL cc_start: 0.7953 (OUTLIER) cc_final: 0.7593 (p) outliers start: 23 outliers final: 19 residues processed: 96 average time/residue: 1.2806 time to fit residues: 129.8061 Evaluate side-chains 97 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.176507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.132821 restraints weight = 8145.832| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.25 r_work: 0.3368 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7367 Z= 0.181 Angle : 0.496 8.110 9969 Z= 0.261 Chirality : 0.040 0.179 1149 Planarity : 0.003 0.039 1255 Dihedral : 4.210 40.625 1003 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.42 % Allowed : 25.22 % Favored : 71.36 % 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 (0.28), residues: 908 helix: 2.36 (0.28), residues: 386 sheet: 1.18 (0.39), residues: 162 loop : -1.89 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS A 182 PHE 0.015 0.001 PHE A 134 TYR 0.010 0.001 TYR A 128 ARG 0.002 0.000 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3017.58 seconds wall clock time: 58 minutes 52.15 seconds (3532.15 seconds total)