Starting phenix.real_space_refine on Wed Feb 12 16:40:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wcm_32424/02_2025/7wcm_32424.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wcm_32424/02_2025/7wcm_32424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wcm_32424/02_2025/7wcm_32424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wcm_32424/02_2025/7wcm_32424.map" model { file = "/net/cci-nas-00/data/ceres_data/7wcm_32424/02_2025/7wcm_32424.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wcm_32424/02_2025/7wcm_32424.cif" } resolution = 2.33 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= 0.000 sd= 0.007 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 57 5.16 5 C 5222 2.51 5 N 1435 2.21 5 O 1518 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8232 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1947 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 2 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 983 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "R" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2240 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 1 Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'8VP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.35, per 1000 atoms: 0.65 Number of scatterers: 8232 At special positions: 0 Unit cell: (81.696, 102.12, 131.054, 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 57 16.00 O 1518 8.00 N 1435 7.00 C 5222 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 155 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 960.3 milliseconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1958 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 45.0% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 9 through 40 Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.663A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.749A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 removed outlier: 4.035A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.551A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.572A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 3.550A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 37 Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.577A pdb=" N ILE B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'C' and resid 9 through 23 removed outlier: 3.831A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.646A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 6 through 36 removed outlier: 3.699A pdb=" N VAL R 25 " --> pdb=" O THR R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 60 removed outlier: 3.583A pdb=" N CYS R 42 " --> pdb=" O GLY R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 68 removed outlier: 3.781A pdb=" N SER R 68 " --> pdb=" O ASP R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 109 removed outlier: 3.966A pdb=" N VAL R 85 " --> pdb=" O ARG R 81 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR R 86 " --> pdb=" O MET R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 117 Processing helix chain 'R' and resid 118 through 139 Processing helix chain 'R' and resid 140 through 143 Processing helix chain 'R' and resid 163 through 173 Processing helix chain 'R' and resid 173 through 210 removed outlier: 3.614A pdb=" N ALA R 177 " --> pdb=" O GLY R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 236 Processing helix chain 'R' and resid 238 through 251 Processing helix chain 'R' and resid 255 through 263 removed outlier: 4.182A pdb=" N VAL R 259 " --> pdb=" O HIS R 255 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU R 261 " --> pdb=" O TYR R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 280 removed outlier: 3.723A pdb=" N LEU R 267 " --> pdb=" O TYR R 263 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER R 272 " --> pdb=" O GLY R 268 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU R 273 " --> pdb=" O VAL R 269 " (cutoff:3.500A) Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 283 through 300 removed outlier: 3.687A pdb=" N LEU R 295 " --> pdb=" O TYR R 291 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY R 296 " --> pdb=" O HIS R 292 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL R 297 " --> pdb=" O MET R 293 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS R 298 " --> pdb=" O ALA R 294 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.449A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 62 removed outlier: 6.798A pdb=" N ILE B 349 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR B 61 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU B 347 " --> pdb=" O THR B 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 74 removed outlier: 3.637A pdb=" N ALA B 71 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU B 90 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA B 103 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE B 92 " --> pdb=" O VAL B 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 116 removed outlier: 6.967A pdb=" N GLY B 126 " --> pdb=" O MET B 112 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N CYS B 114 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA B 124 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TYR B 116 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N TYR B 122 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY B 127 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ILE B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N CYS B 132 " --> pdb=" O GLU B 149 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU B 149 " --> pdb=" O CYS B 132 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE B 134 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG B 145 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 157 through 162 removed outlier: 6.732A pdb=" N SER B 171 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N CYS B 160 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL B 169 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N PHE B 162 " --> pdb=" O GLN B 167 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLN B 167 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE B 168 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP B 181 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLN B 187 " --> pdb=" O ASP B 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 198 through 203 removed outlier: 3.559A pdb=" N SER B 200 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN B 231 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASP B 223 " --> pdb=" O CYS B 229 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N CYS B 229 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 240 through 245 removed outlier: 6.639A pdb=" N CYS B 261 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR B 274 " --> pdb=" O CYS B 261 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU B 263 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN B 270 " --> pdb=" O ASP B 265 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 284 through 289 removed outlier: 3.740A pdb=" N SER B 286 " --> pdb=" O GLY B 299 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ASP B 309 " --> pdb=" O ARG B 315 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG B 315 " --> pdb=" O ASP B 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.790A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1269 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: 2.35 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2690 1.34 - 1.46: 1962 1.46 - 1.58: 3666 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 8400 Sorted by residual: bond pdb=" C20 8VP R 401 " pdb=" N17 8VP R 401 " ideal model delta sigma weight residual 1.357 1.473 -0.116 2.00e-02 2.50e+03 3.39e+01 bond pdb=" C8 8VP R 401 " pdb=" C9 8VP R 401 " ideal model delta sigma weight residual 1.490 1.579 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C9 8VP R 401 " pdb=" N13 8VP R 401 " ideal model delta sigma weight residual 1.378 1.448 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C29 8VP R 401 " pdb=" N28 8VP R 401 " ideal model delta sigma weight residual 1.344 1.401 -0.057 2.00e-02 2.50e+03 8.23e+00 bond pdb=" C3 8VP R 401 " pdb=" N28 8VP R 401 " ideal model delta sigma weight residual 1.423 1.478 -0.055 2.00e-02 2.50e+03 7.62e+00 ... (remaining 8395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 11151 1.80 - 3.60: 175 3.60 - 5.40: 36 5.40 - 7.20: 4 7.20 - 9.00: 3 Bond angle restraints: 11369 Sorted by residual: angle pdb=" N PHE N 108 " pdb=" CA PHE N 108 " pdb=" C PHE N 108 " ideal model delta sigma weight residual 111.24 115.14 -3.90 1.29e+00 6.01e-01 9.12e+00 angle pdb=" C9 8VP R 401 " pdb=" C8 8VP R 401 " pdb=" O7 8VP R 401 " ideal model delta sigma weight residual 107.91 116.91 -9.00 3.00e+00 1.11e-01 8.99e+00 angle pdb=" C16 8VP R 401 " pdb=" N17 8VP R 401 " pdb=" C18 8VP R 401 " ideal model delta sigma weight residual 116.58 107.78 8.80 3.00e+00 1.11e-01 8.60e+00 angle pdb=" C PRO R 144 " pdb=" N MET R 145 " pdb=" CA MET R 145 " ideal model delta sigma weight residual 121.54 126.54 -5.00 1.91e+00 2.74e-01 6.84e+00 angle pdb=" CA ASP A 310 " pdb=" CB ASP A 310 " pdb=" CG ASP A 310 " ideal model delta sigma weight residual 112.60 115.17 -2.57 1.00e+00 1.00e+00 6.60e+00 ... (remaining 11364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4536 17.93 - 35.85: 399 35.85 - 53.78: 49 53.78 - 71.70: 15 71.70 - 89.63: 13 Dihedral angle restraints: 5012 sinusoidal: 1980 harmonic: 3032 Sorted by residual: dihedral pdb=" CA ASP A 310 " pdb=" C ASP A 310 " pdb=" N TYR A 311 " pdb=" CA TYR A 311 " ideal model delta harmonic sigma weight residual 180.00 152.84 27.16 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 -155.68 -24.32 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA GLN B 86 " pdb=" C GLN B 86 " pdb=" N ASP B 87 " pdb=" CA ASP B 87 " ideal model delta harmonic sigma weight residual 180.00 161.36 18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 5009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 852 0.036 - 0.072: 303 0.072 - 0.108: 91 0.108 - 0.144: 32 0.144 - 0.180: 2 Chirality restraints: 1280 Sorted by residual: chirality pdb=" CA VAL N 37 " pdb=" N VAL N 37 " pdb=" C VAL N 37 " pdb=" CB VAL N 37 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.13e-01 chirality pdb=" CA TYR B 70 " pdb=" N TYR B 70 " pdb=" C TYR B 70 " pdb=" CB TYR B 70 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CA ASP A 310 " pdb=" N ASP A 310 " pdb=" C ASP A 310 " pdb=" CB ASP A 310 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 1277 not shown) Planarity restraints: 1448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 70 " -0.027 2.00e-02 2.50e+03 2.03e-02 8.28e+00 pdb=" CG TYR B 70 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR B 70 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 70 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 70 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 70 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 70 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 70 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 246 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO B 247 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 247 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 247 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 183 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C PHE R 183 " -0.032 2.00e-02 2.50e+03 pdb=" O PHE R 183 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE R 184 " 0.011 2.00e-02 2.50e+03 ... (remaining 1445 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2044 2.80 - 3.33: 7580 3.33 - 3.85: 13284 3.85 - 4.38: 15798 4.38 - 4.90: 27122 Nonbonded interactions: 65828 Sorted by model distance: nonbonded pdb=" NE2 GLN A 29 " pdb=" OD1 ASP A 33 " model vdw 2.281 3.120 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 197 " model vdw 2.301 3.120 nonbonded pdb=" O GLN R 148 " pdb=" NZ LYS R 152 " model vdw 2.306 3.120 nonbonded pdb=" O TYR B 96 " pdb=" OG1 THR B 97 " model vdw 2.337 3.040 nonbonded pdb=" OD1 ASN A 292 " pdb=" N LYS A 293 " model vdw 2.356 3.120 ... (remaining 65823 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 22.110 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 0.116 8400 Z= 0.236 Angle : 0.607 8.996 11369 Z= 0.329 Chirality : 0.043 0.180 1280 Planarity : 0.004 0.052 1448 Dihedral : 14.074 89.628 3048 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: 1.05 (0.26), residues: 1031 helix: 1.81 (0.27), residues: 411 sheet: 1.03 (0.35), residues: 208 loop : -0.61 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 93 HIS 0.015 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.049 0.002 TYR B 70 ARG 0.002 0.000 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.844 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 1.6613 time to fit residues: 227.9763 Evaluate side-chains 120 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 79 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN B 279 ASN R 109 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.158139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.107737 restraints weight = 7622.791| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.78 r_work: 0.2977 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8400 Z= 0.303 Angle : 0.709 10.608 11369 Z= 0.390 Chirality : 0.048 0.191 1280 Planarity : 0.005 0.053 1448 Dihedral : 6.594 71.434 1164 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.14 % Allowed : 6.66 % Favored : 91.20 % 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: 1.00 (0.26), residues: 1031 helix: 1.84 (0.25), residues: 419 sheet: 1.03 (0.35), residues: 210 loop : -0.81 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 234 HIS 0.012 0.002 HIS A 357 PHE 0.017 0.002 PHE B 245 TYR 0.017 0.003 TYR A 339 ARG 0.005 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.988 Fit side-chains REVERT: A 300 LYS cc_start: 0.6889 (OUTLIER) cc_final: 0.6401 (mtmt) REVERT: A 314 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6723 (mt-10) REVERT: R 261 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.5926 (mm-30) outliers start: 19 outliers final: 10 residues processed: 126 average time/residue: 1.7386 time to fit residues: 229.3903 Evaluate side-chains 128 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 115 LYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 190 LYS Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 261 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.0270 chunk 38 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 overall best weight: 1.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN N 3 GLN N 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.160211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.112646 restraints weight = 7852.317| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.81 r_work: 0.3039 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8400 Z= 0.178 Angle : 0.571 9.022 11369 Z= 0.314 Chirality : 0.043 0.198 1280 Planarity : 0.004 0.052 1448 Dihedral : 6.126 65.555 1164 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.69 % Allowed : 9.26 % Favored : 89.05 % 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: 1.33 (0.26), residues: 1031 helix: 2.29 (0.26), residues: 418 sheet: 1.05 (0.34), residues: 214 loop : -0.76 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.014 0.002 TYR A 339 ARG 0.004 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.901 Fit side-chains REVERT: A 29 GLN cc_start: 0.8491 (tp40) cc_final: 0.8099 (tp-100) REVERT: A 300 LYS cc_start: 0.6825 (OUTLIER) cc_final: 0.6357 (mtmt) REVERT: A 314 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6678 (mt-10) REVERT: B 70 TYR cc_start: 0.9139 (OUTLIER) cc_final: 0.7669 (m-80) REVERT: C 29 LYS cc_start: 0.8325 (mmtm) cc_final: 0.8002 (mtpp) REVERT: N 3 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7904 (tp-100) REVERT: R 261 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.5932 (mm-30) outliers start: 15 outliers final: 7 residues processed: 126 average time/residue: 1.7466 time to fit residues: 230.1424 Evaluate side-chains 127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 115 LYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 190 LYS Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 261 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 26 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 28 optimal weight: 0.1980 chunk 46 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN N 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.161616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.109420 restraints weight = 7802.333| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.66 r_work: 0.3044 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8400 Z= 0.158 Angle : 0.546 9.670 11369 Z= 0.298 Chirality : 0.042 0.196 1280 Planarity : 0.004 0.051 1448 Dihedral : 5.907 62.905 1164 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.37 % Allowed : 9.37 % Favored : 88.26 % 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: 1.48 (0.26), residues: 1031 helix: 2.49 (0.26), residues: 418 sheet: 1.08 (0.34), residues: 214 loop : -0.76 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.002 0.001 HIS B 102 PHE 0.014 0.001 PHE A 212 TYR 0.014 0.001 TYR A 339 ARG 0.006 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.910 Fit side-chains REVERT: A 29 GLN cc_start: 0.8449 (tp40) cc_final: 0.8042 (tp-100) REVERT: A 300 LYS cc_start: 0.6803 (OUTLIER) cc_final: 0.6334 (mtmt) REVERT: A 314 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6679 (mt-10) REVERT: B 70 TYR cc_start: 0.9135 (OUTLIER) cc_final: 0.7737 (m-80) REVERT: C 29 LYS cc_start: 0.8235 (mmtm) cc_final: 0.7920 (mtpp) REVERT: N 3 GLN cc_start: 0.8151 (tp40) cc_final: 0.7868 (tt0) REVERT: R 115 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7438 (ttpp) REVERT: R 261 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.5910 (mm-30) outliers start: 21 outliers final: 9 residues processed: 129 average time/residue: 1.7024 time to fit residues: 230.0435 Evaluate side-chains 128 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 115 LYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 190 LYS Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 261 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 43 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 16 optimal weight: 0.0770 chunk 100 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 overall best weight: 1.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN N 5 GLN R 197 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.159790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.109454 restraints weight = 7715.110| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.78 r_work: 0.3004 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8400 Z= 0.198 Angle : 0.594 9.483 11369 Z= 0.325 Chirality : 0.044 0.195 1280 Planarity : 0.004 0.052 1448 Dihedral : 5.993 59.779 1164 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.48 % Allowed : 9.59 % Favored : 87.92 % 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: 1.45 (0.26), residues: 1031 helix: 2.49 (0.26), residues: 413 sheet: 1.14 (0.34), residues: 211 loop : -0.79 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 234 HIS 0.003 0.001 HIS B 65 PHE 0.015 0.002 PHE A 212 TYR 0.015 0.002 TYR A 339 ARG 0.006 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.935 Fit side-chains REVERT: A 29 GLN cc_start: 0.8534 (tp40) cc_final: 0.8153 (tp-100) REVERT: A 300 LYS cc_start: 0.6736 (OUTLIER) cc_final: 0.6259 (mtmt) REVERT: A 314 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6694 (mt-10) REVERT: B 70 TYR cc_start: 0.9159 (OUTLIER) cc_final: 0.8336 (m-80) REVERT: C 29 LYS cc_start: 0.8375 (mmtm) cc_final: 0.8051 (mtpp) REVERT: C 32 LYS cc_start: 0.7934 (tttm) cc_final: 0.7680 (mtpm) REVERT: R 261 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.5939 (mm-30) outliers start: 22 outliers final: 10 residues processed: 128 average time/residue: 1.6850 time to fit residues: 225.5557 Evaluate side-chains 127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 115 LYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 190 LYS Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 261 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 28 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN N 5 GLN R 197 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.158024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.110520 restraints weight = 7677.510| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.85 r_work: 0.2996 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8400 Z= 0.298 Angle : 0.698 10.597 11369 Z= 0.381 Chirality : 0.048 0.194 1280 Planarity : 0.005 0.053 1448 Dihedral : 6.247 56.116 1164 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.82 % Allowed : 9.71 % Favored : 87.47 % 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: 1.14 (0.26), residues: 1031 helix: 2.11 (0.25), residues: 413 sheet: 1.16 (0.34), residues: 208 loop : -0.91 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 234 HIS 0.006 0.001 HIS B 65 PHE 0.017 0.002 PHE A 212 TYR 0.016 0.002 TYR A 339 ARG 0.006 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.961 Fit side-chains REVERT: A 300 LYS cc_start: 0.6757 (OUTLIER) cc_final: 0.6263 (mtmt) REVERT: A 314 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6728 (mt-10) REVERT: A 370 GLU cc_start: 0.5975 (mp0) cc_final: 0.5734 (tp30) REVERT: B 70 TYR cc_start: 0.9149 (OUTLIER) cc_final: 0.8557 (m-80) REVERT: B 96 TYR cc_start: 0.7740 (OUTLIER) cc_final: 0.6279 (m-10) REVERT: R 261 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.5936 (mm-30) outliers start: 25 outliers final: 12 residues processed: 130 average time/residue: 1.7370 time to fit residues: 236.3631 Evaluate side-chains 132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 115 LYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 190 LYS Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 261 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 42 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 55 optimal weight: 0.0770 chunk 10 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN B 277 HIS N 3 GLN R 197 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.159946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.107538 restraints weight = 7696.469| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.65 r_work: 0.3013 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8400 Z= 0.199 Angle : 0.598 9.035 11369 Z= 0.327 Chirality : 0.044 0.196 1280 Planarity : 0.004 0.053 1448 Dihedral : 5.984 54.403 1164 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.26 % Allowed : 11.06 % Favored : 86.68 % 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: 1.35 (0.26), residues: 1031 helix: 2.38 (0.26), residues: 413 sheet: 1.16 (0.34), residues: 211 loop : -0.87 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 234 HIS 0.003 0.001 HIS B 277 PHE 0.015 0.002 PHE A 212 TYR 0.015 0.002 TYR A 339 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.907 Fit side-chains REVERT: A 29 GLN cc_start: 0.8448 (tp40) cc_final: 0.8151 (tp-100) REVERT: A 300 LYS cc_start: 0.6681 (OUTLIER) cc_final: 0.6206 (mtmt) REVERT: A 314 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6668 (mt-10) REVERT: B 70 TYR cc_start: 0.9152 (OUTLIER) cc_final: 0.8412 (m-80) REVERT: R 261 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.5896 (mm-30) outliers start: 20 outliers final: 10 residues processed: 127 average time/residue: 1.8104 time to fit residues: 241.0249 Evaluate side-chains 128 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 115 LYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 190 LYS Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 261 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN B 277 HIS N 3 GLN R 197 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.160424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.108040 restraints weight = 7733.523| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.64 r_work: 0.3020 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8400 Z= 0.188 Angle : 0.584 8.929 11369 Z= 0.319 Chirality : 0.044 0.196 1280 Planarity : 0.004 0.053 1448 Dihedral : 5.895 52.517 1164 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.14 % Allowed : 11.17 % Favored : 86.68 % 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: 1.44 (0.26), residues: 1031 helix: 2.50 (0.26), residues: 412 sheet: 1.18 (0.34), residues: 211 loop : -0.84 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 234 HIS 0.003 0.001 HIS B 277 PHE 0.015 0.001 PHE A 212 TYR 0.015 0.002 TYR A 339 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 1.014 Fit side-chains REVERT: A 29 GLN cc_start: 0.8399 (tp40) cc_final: 0.8168 (tp-100) REVERT: A 300 LYS cc_start: 0.6704 (OUTLIER) cc_final: 0.6219 (mtmt) REVERT: A 314 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6680 (mt-10) REVERT: B 70 TYR cc_start: 0.9148 (OUTLIER) cc_final: 0.8344 (m-80) REVERT: R 261 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.5897 (mm-30) outliers start: 19 outliers final: 10 residues processed: 122 average time/residue: 1.8367 time to fit residues: 234.2555 Evaluate side-chains 125 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 115 LYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 190 LYS Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 261 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 48 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN B 277 HIS N 3 GLN R 197 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.161531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.109121 restraints weight = 7821.282| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.66 r_work: 0.3039 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 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 0.033 8400 Z= 0.166 Angle : 0.556 8.470 11369 Z= 0.303 Chirality : 0.043 0.196 1280 Planarity : 0.004 0.052 1448 Dihedral : 5.742 50.268 1164 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.14 % Allowed : 11.74 % Favored : 86.12 % 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: 1.56 (0.26), residues: 1031 helix: 2.65 (0.26), residues: 411 sheet: 1.07 (0.34), residues: 217 loop : -0.75 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.004 0.001 HIS B 277 PHE 0.014 0.001 PHE A 212 TYR 0.014 0.001 TYR A 339 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.999 Fit side-chains REVERT: A 300 LYS cc_start: 0.6673 (OUTLIER) cc_final: 0.6189 (mtmt) REVERT: A 314 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6670 (mt-10) REVERT: B 70 TYR cc_start: 0.9138 (OUTLIER) cc_final: 0.8267 (m-80) REVERT: C 29 LYS cc_start: 0.8240 (mmtm) cc_final: 0.7938 (mtpp) REVERT: R 261 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.5933 (mm-30) outliers start: 19 outliers final: 11 residues processed: 122 average time/residue: 1.7300 time to fit residues: 220.9087 Evaluate side-chains 121 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 115 LYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 190 LYS Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 261 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 28 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN B 277 HIS N 3 GLN R 197 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.162314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.112880 restraints weight = 7705.715| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.90 r_work: 0.3037 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8400 Z= 0.154 Angle : 0.543 8.497 11369 Z= 0.295 Chirality : 0.042 0.200 1280 Planarity : 0.004 0.052 1448 Dihedral : 5.632 48.789 1164 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.58 % Allowed : 12.42 % Favored : 86.00 % 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: 1.64 (0.26), residues: 1031 helix: 2.74 (0.26), residues: 411 sheet: 1.08 (0.34), residues: 217 loop : -0.71 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.004 0.001 HIS B 277 PHE 0.014 0.001 PHE A 212 TYR 0.014 0.001 TYR A 339 ARG 0.005 0.000 ARG A 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.916 Fit side-chains REVERT: A 300 LYS cc_start: 0.6666 (OUTLIER) cc_final: 0.6193 (mtmt) REVERT: A 314 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6703 (mt-10) REVERT: B 70 TYR cc_start: 0.9148 (OUTLIER) cc_final: 0.8269 (m-80) REVERT: C 21 MET cc_start: 0.7556 (tpp) cc_final: 0.7003 (ttt) REVERT: C 29 LYS cc_start: 0.8213 (mmtm) cc_final: 0.7926 (mtpp) REVERT: R 115 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7439 (ttpp) outliers start: 14 outliers final: 7 residues processed: 121 average time/residue: 1.6953 time to fit residues: 214.9381 Evaluate side-chains 121 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 115 LYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 190 LYS Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 259 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 24 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN N 3 GLN N 5 GLN R 197 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.160360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.107697 restraints weight = 7822.505| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.66 r_work: 0.3018 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8400 Z= 0.202 Angle : 0.604 9.443 11369 Z= 0.327 Chirality : 0.044 0.198 1280 Planarity : 0.004 0.052 1448 Dihedral : 5.831 48.848 1164 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.69 % Allowed : 12.19 % Favored : 86.12 % 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: 1.50 (0.26), residues: 1031 helix: 2.55 (0.26), residues: 412 sheet: 1.21 (0.34), residues: 211 loop : -0.80 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 234 HIS 0.003 0.001 HIS B 65 PHE 0.015 0.002 PHE A 212 TYR 0.015 0.002 TYR A 339 ARG 0.005 0.000 ARG A 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8833.73 seconds wall clock time: 155 minutes 42.52 seconds (9342.52 seconds total)