Starting phenix.real_space_refine on Wed Aug 5 02:44:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/24ti_69804/08_2026/24ti_69804_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/24ti_69804/08_2026/24ti_69804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/24ti_69804/08_2026/24ti_69804_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/24ti_69804/08_2026/24ti_69804_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/24ti_69804/08_2026/24ti_69804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/24ti_69804/08_2026/24ti_69804.map" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.019 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: 5 Type Number sf(0) Gaussians S 45 5.16 5 C 5059 2.51 5 N 1394 2.21 5 O 1469 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7970 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2036 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain breaks: 2 Chain: "A" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1893 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 3 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain: "R" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'KHF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.46, per 1000 atoms: 0.18 Number of scatterers: 7970 At special positions: 0 Unit cell: (76.041, 103.887, 124.236, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 F 3 9.00 O 1469 8.00 N 1394 7.00 C 5059 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 202 " - pdb=" SG CYS R 272 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 358.8 milliseconds 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1880 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 11 sheets defined 39.8% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'R' and resid 127 through 153 removed outlier: 4.004A pdb=" N ALA R 153 " --> pdb=" O THR R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 158 removed outlier: 4.276A pdb=" N HIS R 158 " --> pdb=" O ARG R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 159 through 187 removed outlier: 3.967A pdb=" N VAL R 179 " --> pdb=" O LYS R 175 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE R 180 " --> pdb=" O ALA R 176 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU R 181 " --> pdb=" O GLY R 177 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS R 182 " --> pdb=" O ALA R 178 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE R 187 " --> pdb=" O ASP R 183 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 232 Processing helix chain 'R' and resid 239 through 268 removed outlier: 3.685A pdb=" N TRP R 250 " --> pdb=" O VAL R 246 " (cutoff:3.500A) Proline residue: R 253 - end of helix Processing helix chain 'R' and resid 270 through 274 Processing helix chain 'R' and resid 282 through 311 Proline residue: R 288 - end of helix Processing helix chain 'R' and resid 324 through 332 Processing helix chain 'R' and resid 336 through 346 removed outlier: 3.535A pdb=" N TYR R 342 " --> pdb=" O PHE R 338 " (cutoff:3.500A) Processing helix chain 'R' and resid 358 through 362 Processing helix chain 'R' and resid 363 through 366 Processing helix chain 'R' and resid 367 through 377 removed outlier: 3.625A pdb=" N ALA R 373 " --> pdb=" O GLY R 369 " (cutoff:3.500A) Processing helix chain 'R' and resid 380 through 394 removed outlier: 3.586A pdb=" N GLU R 386 " --> pdb=" O GLU R 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 39 removed outlier: 3.504A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 4.212A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.995A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.524A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.919A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.604A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 36 removed outlier: 4.510A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 22 removed outlier: 4.123A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG G 13 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.433A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.523A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.500A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.058A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.514A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.622A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 Processing sheet with id=AA8, first strand: chain 'B' and resid 250 through 251 Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.686A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.559A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1083 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1293 1.31 - 1.44: 2285 1.44 - 1.57: 4501 1.57 - 1.71: 1 1.71 - 1.84: 61 Bond restraints: 8141 Sorted by residual: bond pdb=" C16 KHF R 601 " pdb=" N2 KHF R 601 " ideal model delta sigma weight residual 1.274 1.484 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C17 KHF R 601 " pdb=" O3 KHF R 601 " ideal model delta sigma weight residual 1.208 1.394 -0.186 2.00e-02 2.50e+03 8.61e+01 bond pdb=" C25 KHF R 601 " pdb=" N5 KHF R 601 " ideal model delta sigma weight residual 1.392 1.550 -0.158 2.00e-02 2.50e+03 6.23e+01 bond pdb=" C23 KHF R 601 " pdb=" C24 KHF R 601 " ideal model delta sigma weight residual 1.388 1.537 -0.149 2.00e-02 2.50e+03 5.57e+01 bond pdb=" C5 KHF R 601 " pdb=" C6 KHF R 601 " ideal model delta sigma weight residual 1.391 1.536 -0.145 2.00e-02 2.50e+03 5.26e+01 ... (remaining 8136 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 11005 3.37 - 6.73: 27 6.73 - 10.10: 3 10.10 - 13.46: 1 13.46 - 16.83: 3 Bond angle restraints: 11039 Sorted by residual: angle pdb=" C18 KHF R 601 " pdb=" C16 KHF R 601 " pdb=" N2 KHF R 601 " ideal model delta sigma weight residual 123.58 140.41 -16.83 3.00e+00 1.11e-01 3.15e+01 angle pdb=" O1 KHF R 601 " pdb=" S1 KHF R 601 " pdb=" O2 KHF R 601 " ideal model delta sigma weight residual 118.72 101.98 16.74 3.00e+00 1.11e-01 3.12e+01 angle pdb=" C26 KHF R 601 " pdb=" C27 KHF R 601 " pdb=" N4 KHF R 601 " ideal model delta sigma weight residual 101.01 114.93 -13.92 3.00e+00 1.11e-01 2.15e+01 angle pdb=" C18 KHF R 601 " pdb=" C16 KHF R 601 " pdb=" N3 KHF R 601 " ideal model delta sigma weight residual 122.36 110.65 11.71 3.00e+00 1.11e-01 1.52e+01 angle pdb=" CA PRO G 60 " pdb=" N PRO G 60 " pdb=" CD PRO G 60 " ideal model delta sigma weight residual 112.00 106.73 5.27 1.40e+00 5.10e-01 1.41e+01 ... (remaining 11034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.69: 4373 24.69 - 49.38: 394 49.38 - 74.06: 53 74.06 - 98.75: 11 98.75 - 123.44: 8 Dihedral angle restraints: 4839 sinusoidal: 1936 harmonic: 2903 Sorted by residual: dihedral pdb=" CA ALA R 153 " pdb=" C ALA R 153 " pdb=" N LEU R 154 " pdb=" CA LEU R 154 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" C25 KHF R 601 " pdb=" C27 KHF R 601 " pdb=" N4 KHF R 601 " pdb=" C29 KHF R 601 " ideal model delta sinusoidal sigma weight residual 116.77 -119.79 -123.44 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" C28 KHF R 601 " pdb=" C27 KHF R 601 " pdb=" N4 KHF R 601 " pdb=" C4 KHF R 601 " ideal model delta sinusoidal sigma weight residual -64.48 57.47 -121.95 1 3.00e+01 1.11e-03 1.63e+01 ... (remaining 4836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 757 0.026 - 0.052: 301 0.052 - 0.078: 95 0.078 - 0.104: 48 0.104 - 0.130: 30 Chirality restraints: 1231 Sorted by residual: chirality pdb=" CA ILE R 335 " pdb=" N ILE R 335 " pdb=" C ILE R 335 " pdb=" CB ILE R 335 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 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 2.57 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE B 123 " pdb=" N ILE B 123 " pdb=" C ILE B 123 " pdb=" CB ILE B 123 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 1228 not shown) Planarity restraints: 1400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 KHF R 601 " -0.034 2.00e-02 2.50e+03 8.36e-02 1.22e+02 pdb=" C16 KHF R 601 " 0.076 2.00e-02 2.50e+03 pdb=" C17 KHF R 601 " -0.021 2.00e-02 2.50e+03 pdb=" C18 KHF R 601 " 0.050 2.00e-02 2.50e+03 pdb=" N2 KHF R 601 " -0.005 2.00e-02 2.50e+03 pdb=" N3 KHF R 601 " -0.168 2.00e-02 2.50e+03 pdb=" O3 KHF R 601 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN G 59 " -0.034 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO G 60 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 348 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO R 349 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO R 349 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 349 " 0.017 5.00e-02 4.00e+02 ... (remaining 1397 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 74 2.49 - 3.09: 5875 3.09 - 3.70: 12027 3.70 - 4.30: 18242 4.30 - 4.90: 31120 Nonbonded interactions: 67338 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 1.890 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 1.982 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.041 3.040 nonbonded pdb=" OG SER R 140 " pdb=" O SER R 366 " model vdw 2.054 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.070 3.040 ... (remaining 67333 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.050 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 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 : 0.012 0.877 8143 Z= 1.031 Angle : 0.562 16.829 11041 Z= 0.262 Chirality : 0.038 0.130 1231 Planarity : 0.003 0.084 1400 Dihedral : 18.895 123.440 2956 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 28.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 6.32 % Allowed : 26.67 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.27), residues: 983 helix: 2.48 (0.28), residues: 364 sheet: 0.34 (0.33), residues: 226 loop : -0.68 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 356 TYR 0.007 0.001 TYR G 40 PHE 0.012 0.001 PHE N 108 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00701 / 0.34 ( 8141) covalent geometry : angle 0.56205 / 0.26 (11039) SS BOND : bond 0.00271 / 0.14 ( 1) SS BOND : angle 0.66158 / 0.36 ( 2) hydrogen bonds : bond 0.12257 / 8.60 ( 385) hydrogen bonds : angle 5.12788 / 3.66 ( 1083) Misc. bond : bond 0.87688 / 46.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 207 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 286 LYS cc_start: 0.8775 (tttp) cc_final: 0.8519 (ttmp) REVERT: R 386 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8299 (tm-30) REVERT: A 27 GLU cc_start: 0.7603 (mp0) cc_final: 0.7163 (mp0) REVERT: B 17 GLN cc_start: 0.9427 (tm-30) cc_final: 0.9212 (tm-30) REVERT: B 32 GLN cc_start: 0.8245 (mt0) cc_final: 0.7595 (mp10) REVERT: B 61 MET cc_start: 0.9370 (ppp) cc_final: 0.9119 (ppp) REVERT: B 132 ASN cc_start: 0.8370 (m110) cc_final: 0.8089 (p0) REVERT: B 301 LYS cc_start: 0.8983 (mmmt) cc_final: 0.8756 (mmtm) REVERT: G 21 MET cc_start: 0.8345 (mpt) cc_final: 0.7902 (mpp) REVERT: G 29 LYS cc_start: 0.8915 (mmtm) cc_final: 0.8658 (mptp) REVERT: G 30 VAL cc_start: 0.9339 (t) cc_final: 0.9058 (p) REVERT: G 54 VAL cc_start: 0.9013 (m) cc_final: 0.8803 (p) REVERT: G 55 PRO cc_start: 0.8719 (Cg_exo) cc_final: 0.7844 (Cg_endo) REVERT: G 58 GLU cc_start: 0.8352 (pm20) cc_final: 0.7639 (pm20) REVERT: N 28 THR cc_start: 0.8437 (m) cc_final: 0.7916 (p) REVERT: N 38 ARG cc_start: 0.8216 (ptt180) cc_final: 0.7895 (ttp80) REVERT: N 85 SER cc_start: 0.8884 (m) cc_final: 0.8631 (p) outliers start: 54 outliers final: 37 residues processed: 244 average time/residue: 0.5210 time to fit residues: 134.5344 Evaluate side-chains 206 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 TYR Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 209 SER Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 335 ILE Chi-restraints excluded: chain R residue 343 ILE Chi-restraints excluded: chain R residue 362 LEU Chi-restraints excluded: chain R residue 370 PHE Chi-restraints excluded: chain R residue 371 ILE Chi-restraints excluded: chain R residue 383 VAL Chi-restraints excluded: chain R residue 388 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 78 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.0670 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 368 GLN ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN A 213 GLN B 75 GLN B 239 ASN G 59 ASN N 74 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.124951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.088949 restraints weight = 13306.256| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.28 r_work: 0.2974 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8143 Z= 0.142 Angle : 0.592 8.115 11041 Z= 0.311 Chirality : 0.042 0.147 1231 Planarity : 0.004 0.041 1400 Dihedral : 13.417 130.057 1198 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 6.20 % Allowed : 28.30 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.27), residues: 983 helix: 2.47 (0.27), residues: 358 sheet: 0.51 (0.34), residues: 220 loop : -0.65 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 309 TYR 0.010 0.001 TYR R 133 PHE 0.016 0.001 PHE R 370 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 8141) covalent geometry : angle 0.59210 / 0.31 (11039) SS BOND : bond 0.00089 / 0.05 ( 1) SS BOND : angle 0.55587 / 0.32 ( 2) hydrogen bonds : bond 0.04083 / 2.65 ( 385) hydrogen bonds : angle 4.28814 / 3.09 ( 1083) Misc. bond : bond 0.00251 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 180 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 281 TYR cc_start: 0.8148 (m-80) cc_final: 0.7619 (m-80) REVERT: R 309 ARG cc_start: 0.8300 (ttm-80) cc_final: 0.8060 (ttm-80) REVERT: R 332 LEU cc_start: 0.8684 (tt) cc_final: 0.8412 (tm) REVERT: R 386 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8097 (tm-30) REVERT: A 14 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.8369 (p0) REVERT: A 16 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: A 239 ASN cc_start: 0.9266 (OUTLIER) cc_final: 0.9018 (p0) REVERT: A 280 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8315 (tttm) REVERT: A 339 TYR cc_start: 0.7953 (m-80) cc_final: 0.7617 (m-80) REVERT: A 356 ARG cc_start: 0.8696 (mtm-85) cc_final: 0.8466 (mtm110) REVERT: B 17 GLN cc_start: 0.9245 (tm-30) cc_final: 0.9044 (tm-30) REVERT: B 20 ASP cc_start: 0.9489 (m-30) cc_final: 0.9200 (m-30) REVERT: B 132 ASN cc_start: 0.8661 (m110) cc_final: 0.8121 (p0) REVERT: B 217 MET cc_start: 0.8195 (pmm) cc_final: 0.7867 (pmm) REVERT: B 234 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.8034 (t80) REVERT: B 260 GLU cc_start: 0.8323 (pt0) cc_final: 0.7529 (tt0) REVERT: B 262 MET cc_start: 0.8394 (tpp) cc_final: 0.7633 (tpp) REVERT: B 301 LYS cc_start: 0.8707 (mmmt) cc_final: 0.8303 (mmmm) REVERT: G 14 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8609 (mmtt) REVERT: G 46 LYS cc_start: 0.8784 (mtmm) cc_final: 0.8582 (tptp) REVERT: G 47 GLU cc_start: 0.8430 (mt-10) cc_final: 0.7864 (mm-30) REVERT: G 54 VAL cc_start: 0.8771 (m) cc_final: 0.8345 (p) REVERT: G 55 PRO cc_start: 0.8543 (Cg_exo) cc_final: 0.7819 (Cg_endo) REVERT: G 58 GLU cc_start: 0.8377 (pm20) cc_final: 0.7825 (pm20) REVERT: N 28 THR cc_start: 0.8095 (m) cc_final: 0.7462 (p) REVERT: N 53 GLN cc_start: 0.8538 (mp10) cc_final: 0.8319 (mp10) REVERT: N 117 TYR cc_start: 0.7708 (m-80) cc_final: 0.7504 (m-10) outliers start: 53 outliers final: 17 residues processed: 215 average time/residue: 0.5282 time to fit residues: 120.1232 Evaluate side-chains 183 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 TYR Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 335 ILE Chi-restraints excluded: chain R residue 362 LEU Chi-restraints excluded: chain R residue 370 PHE Chi-restraints excluded: chain R residue 371 ILE Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 59 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.0070 chunk 93 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.0980 chunk 37 optimal weight: 0.3980 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 213 GLN A 390 GLN B 13 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.126206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.090739 restraints weight = 13064.846| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.25 r_work: 0.2991 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8143 Z= 0.112 Angle : 0.550 7.477 11041 Z= 0.289 Chirality : 0.042 0.176 1231 Planarity : 0.004 0.038 1400 Dihedral : 12.599 129.387 1161 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.98 % Allowed : 31.11 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.27), residues: 983 helix: 2.52 (0.27), residues: 352 sheet: 0.65 (0.34), residues: 219 loop : -0.58 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 389 TYR 0.014 0.001 TYR N 60 PHE 0.015 0.001 PHE N 108 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS R 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 8141) covalent geometry : angle 0.54998 / 0.29 (11039) SS BOND : bond 0.00063 / 0.03 ( 1) SS BOND : angle 0.37778 / 0.20 ( 2) hydrogen bonds : bond 0.03764 / 2.44 ( 385) hydrogen bonds : angle 4.08293 / 2.96 ( 1083) Misc. bond : bond 0.00166 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 182 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7942 (mmmm) REVERT: R 183 ASP cc_start: 0.8309 (m-30) cc_final: 0.8051 (m-30) REVERT: R 281 TYR cc_start: 0.8005 (m-80) cc_final: 0.7778 (m-80) REVERT: R 286 LYS cc_start: 0.7614 (tttp) cc_final: 0.7317 (ttmp) REVERT: R 332 LEU cc_start: 0.8652 (tt) cc_final: 0.8376 (tm) REVERT: R 350 ASP cc_start: 0.8164 (t0) cc_final: 0.7901 (t70) REVERT: R 386 GLU cc_start: 0.8284 (tm-30) cc_final: 0.8059 (tm-30) REVERT: A 16 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: A 23 ASN cc_start: 0.7723 (t0) cc_final: 0.7340 (t0) REVERT: A 27 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7194 (mp0) REVERT: A 213 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8878 (mt0) REVERT: A 280 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8359 (tttm) REVERT: A 339 TYR cc_start: 0.7943 (m-80) cc_final: 0.7503 (m-80) REVERT: B 17 GLN cc_start: 0.9264 (tm-30) cc_final: 0.9014 (tm-30) REVERT: B 32 GLN cc_start: 0.7935 (mp10) cc_final: 0.7498 (mp10) REVERT: B 132 ASN cc_start: 0.8707 (m110) cc_final: 0.8255 (p0) REVERT: B 138 GLU cc_start: 0.8970 (tp30) cc_final: 0.8737 (tp30) REVERT: B 217 MET cc_start: 0.8239 (pmm) cc_final: 0.7805 (pmm) REVERT: B 234 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8150 (t80) REVERT: B 260 GLU cc_start: 0.8291 (pt0) cc_final: 0.7537 (tt0) REVERT: B 262 MET cc_start: 0.8285 (tpp) cc_final: 0.7570 (tpp) REVERT: G 14 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8616 (mmtt) REVERT: G 47 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8089 (mm-30) REVERT: G 54 VAL cc_start: 0.8746 (m) cc_final: 0.8521 (p) REVERT: G 58 GLU cc_start: 0.8346 (pm20) cc_final: 0.8006 (pm20) REVERT: N 28 THR cc_start: 0.7924 (m) cc_final: 0.7415 (p) REVERT: N 53 GLN cc_start: 0.8562 (mp10) cc_final: 0.8282 (mp10) REVERT: N 80 TYR cc_start: 0.7902 (m-80) cc_final: 0.7642 (m-80) outliers start: 34 outliers final: 15 residues processed: 191 average time/residue: 0.4665 time to fit residues: 94.6144 Evaluate side-chains 180 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 TYR Chi-restraints excluded: chain R residue 145 PHE Chi-restraints excluded: chain R residue 182 LYS Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 335 ILE Chi-restraints excluded: chain R residue 341 HIS Chi-restraints excluded: chain R residue 362 LEU Chi-restraints excluded: chain R residue 370 PHE Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 61 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 32 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.123321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.087811 restraints weight = 13445.116| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.27 r_work: 0.2938 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8143 Z= 0.169 Angle : 0.592 9.273 11041 Z= 0.304 Chirality : 0.043 0.183 1231 Planarity : 0.004 0.041 1400 Dihedral : 12.592 130.512 1155 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.56 % Allowed : 30.29 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.27), residues: 983 helix: 2.13 (0.27), residues: 359 sheet: 0.60 (0.34), residues: 220 loop : -0.46 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 19 TYR 0.013 0.001 TYR N 60 PHE 0.015 0.001 PHE R 370 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS R 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 8141) covalent geometry : angle 0.59240 / 0.30 (11039) SS BOND : bond 0.00142 / 0.07 ( 1) SS BOND : angle 0.77576 / 0.41 ( 2) hydrogen bonds : bond 0.04044 / 2.60 ( 385) hydrogen bonds : angle 4.03630 / 2.93 ( 1083) Misc. bond : bond 0.00194 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 165 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 182 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7884 (mmmm) REVERT: R 183 ASP cc_start: 0.8265 (m-30) cc_final: 0.8019 (m-30) REVERT: R 281 TYR cc_start: 0.8048 (m-80) cc_final: 0.7840 (m-80) REVERT: A 15 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8378 (mm-30) REVERT: A 16 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: A 213 GLN cc_start: 0.9255 (OUTLIER) cc_final: 0.9030 (mt0) REVERT: A 283 ARG cc_start: 0.8061 (ptp-170) cc_final: 0.7580 (ptp90) REVERT: A 339 TYR cc_start: 0.8140 (m-80) cc_final: 0.7674 (m-80) REVERT: B 32 GLN cc_start: 0.7930 (mp10) cc_final: 0.7482 (mp10) REVERT: B 132 ASN cc_start: 0.8732 (m110) cc_final: 0.8244 (p0) REVERT: B 217 MET cc_start: 0.8272 (pmm) cc_final: 0.7767 (pmm) REVERT: B 234 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.8179 (t80) REVERT: B 262 MET cc_start: 0.8309 (tpp) cc_final: 0.7780 (tpp) REVERT: G 14 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8662 (mmpt) REVERT: G 21 MET cc_start: 0.8379 (ttp) cc_final: 0.7966 (ttt) REVERT: G 46 LYS cc_start: 0.9104 (tptp) cc_final: 0.8847 (tppp) REVERT: G 47 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8085 (mm-30) REVERT: G 54 VAL cc_start: 0.8795 (m) cc_final: 0.8287 (p) REVERT: G 58 GLU cc_start: 0.8346 (pm20) cc_final: 0.7844 (pm20) REVERT: N 28 THR cc_start: 0.7996 (m) cc_final: 0.7469 (p) REVERT: N 47 TRP cc_start: 0.7343 (t60) cc_final: 0.7112 (t60) REVERT: N 53 GLN cc_start: 0.8581 (mp10) cc_final: 0.8294 (mp10) REVERT: N 90 ASP cc_start: 0.7307 (m-30) cc_final: 0.6883 (m-30) outliers start: 39 outliers final: 19 residues processed: 189 average time/residue: 0.5120 time to fit residues: 102.4875 Evaluate side-chains 177 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 TYR Chi-restraints excluded: chain R residue 145 PHE Chi-restraints excluded: chain R residue 159 CYS Chi-restraints excluded: chain R residue 182 LYS Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 335 ILE Chi-restraints excluded: chain R residue 341 HIS Chi-restraints excluded: chain R residue 362 LEU Chi-restraints excluded: chain R residue 370 PHE Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 94 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 0.0670 chunk 91 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 158 HIS R 341 HIS ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.123390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.088817 restraints weight = 13416.351| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.14 r_work: 0.2968 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8143 Z= 0.162 Angle : 0.572 7.755 11041 Z= 0.302 Chirality : 0.043 0.197 1231 Planarity : 0.004 0.041 1400 Dihedral : 12.505 130.137 1155 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.26 % Allowed : 28.77 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.27), residues: 983 helix: 1.99 (0.27), residues: 359 sheet: 0.62 (0.34), residues: 220 loop : -0.41 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 27 TYR 0.013 0.001 TYR N 60 PHE 0.019 0.001 PHE N 108 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 8141) covalent geometry : angle 0.57198 / 0.30 (11039) SS BOND : bond 0.00235 / 0.12 ( 1) SS BOND : angle 0.82217 / 0.44 ( 2) hydrogen bonds : bond 0.04029 / 2.61 ( 385) hydrogen bonds : angle 4.01735 / 2.92 ( 1083) Misc. bond : bond 0.00201 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 167 GLN cc_start: 0.8502 (mt0) cc_final: 0.8299 (mt0) REVERT: R 182 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7794 (mmmm) REVERT: R 183 ASP cc_start: 0.8263 (m-30) cc_final: 0.8000 (m-30) REVERT: A 15 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8337 (mm-30) REVERT: A 16 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7787 (mp0) REVERT: A 213 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8580 (tt0) REVERT: A 280 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8016 (tttm) REVERT: A 283 ARG cc_start: 0.8081 (ptp-170) cc_final: 0.7549 (ptp90) REVERT: A 339 TYR cc_start: 0.8159 (m-80) cc_final: 0.7717 (m-80) REVERT: B 32 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7585 (mp10) REVERT: B 42 ARG cc_start: 0.8293 (tpp80) cc_final: 0.7701 (tmm-80) REVERT: B 132 ASN cc_start: 0.8641 (m110) cc_final: 0.8208 (p0) REVERT: B 153 ASP cc_start: 0.8479 (m-30) cc_final: 0.7736 (p0) REVERT: B 217 MET cc_start: 0.8356 (pmm) cc_final: 0.7898 (pmm) REVERT: B 234 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8214 (t80) REVERT: B 260 GLU cc_start: 0.8464 (pt0) cc_final: 0.7792 (tt0) REVERT: B 262 MET cc_start: 0.8401 (tpp) cc_final: 0.7676 (tpp) REVERT: G 14 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8697 (mmpt) REVERT: G 21 MET cc_start: 0.8395 (ttp) cc_final: 0.7903 (ttt) REVERT: G 42 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8428 (mm-30) REVERT: G 46 LYS cc_start: 0.9078 (tptp) cc_final: 0.8712 (tppp) REVERT: G 47 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8161 (mm-30) REVERT: N 28 THR cc_start: 0.7928 (m) cc_final: 0.7444 (p) REVERT: N 38 ARG cc_start: 0.7985 (ptp90) cc_final: 0.7709 (ttp-170) REVERT: N 47 TRP cc_start: 0.7407 (t60) cc_final: 0.7192 (t60) REVERT: N 53 GLN cc_start: 0.8553 (mp10) cc_final: 0.8301 (mp10) REVERT: N 90 ASP cc_start: 0.7258 (m-30) cc_final: 0.7049 (m-30) outliers start: 45 outliers final: 21 residues processed: 188 average time/residue: 0.4823 time to fit residues: 96.4761 Evaluate side-chains 183 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 TYR Chi-restraints excluded: chain R residue 145 PHE Chi-restraints excluded: chain R residue 159 CYS Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 182 LYS Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 335 ILE Chi-restraints excluded: chain R residue 341 HIS Chi-restraints excluded: chain R residue 370 PHE Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 68 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 15 optimal weight: 0.0470 chunk 73 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 158 HIS A 213 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.123807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.088961 restraints weight = 13231.861| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.14 r_work: 0.2982 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8143 Z= 0.133 Angle : 0.574 7.558 11041 Z= 0.302 Chirality : 0.043 0.179 1231 Planarity : 0.004 0.041 1400 Dihedral : 12.454 129.861 1153 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.03 % Allowed : 28.89 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.27), residues: 983 helix: 2.07 (0.27), residues: 359 sheet: 0.63 (0.34), residues: 220 loop : -0.43 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 27 TYR 0.015 0.001 TYR N 60 PHE 0.015 0.001 PHE N 27 TRP 0.016 0.001 TRP B 82 HIS 0.015 0.001 HIS R 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 8141) covalent geometry : angle 0.57403 / 0.30 (11039) SS BOND : bond 0.00149 / 0.08 ( 1) SS BOND : angle 0.69374 / 0.37 ( 2) hydrogen bonds : bond 0.03856 / 2.49 ( 385) hydrogen bonds : angle 3.96361 / 2.89 ( 1083) Misc. bond : bond 0.00146 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 163 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 182 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7707 (mmmm) REVERT: R 183 ASP cc_start: 0.8259 (m-30) cc_final: 0.7997 (m-30) REVERT: A 15 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8378 (mm-30) REVERT: A 16 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7788 (mp0) REVERT: A 213 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8546 (tt0) REVERT: A 280 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8041 (tttm) REVERT: A 283 ARG cc_start: 0.8066 (ptp-170) cc_final: 0.7523 (ptp90) REVERT: A 339 TYR cc_start: 0.8137 (m-80) cc_final: 0.7657 (m-80) REVERT: B 32 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7573 (mp10) REVERT: B 132 ASN cc_start: 0.8627 (m110) cc_final: 0.8211 (p0) REVERT: B 153 ASP cc_start: 0.8477 (m-30) cc_final: 0.7743 (p0) REVERT: B 217 MET cc_start: 0.8365 (pmm) cc_final: 0.7885 (pmm) REVERT: B 234 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8269 (t80) REVERT: B 260 GLU cc_start: 0.8410 (pt0) cc_final: 0.7711 (tt0) REVERT: B 262 MET cc_start: 0.8366 (tpp) cc_final: 0.7648 (tpp) REVERT: G 14 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8666 (mmtm) REVERT: G 21 MET cc_start: 0.8404 (ttp) cc_final: 0.7956 (ttt) REVERT: G 46 LYS cc_start: 0.9054 (tptp) cc_final: 0.8716 (tppp) REVERT: G 47 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8133 (mm-30) REVERT: N 28 THR cc_start: 0.7922 (m) cc_final: 0.7309 (p) REVERT: N 38 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7454 (ttp80) REVERT: N 53 GLN cc_start: 0.8544 (mp10) cc_final: 0.8290 (mp10) REVERT: N 87 LYS cc_start: 0.7849 (mttm) cc_final: 0.7581 (mtmm) REVERT: N 90 ASP cc_start: 0.7326 (m-30) cc_final: 0.7023 (m-30) outliers start: 43 outliers final: 20 residues processed: 189 average time/residue: 0.4932 time to fit residues: 99.2876 Evaluate side-chains 182 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 TYR Chi-restraints excluded: chain R residue 145 PHE Chi-restraints excluded: chain R residue 159 CYS Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 182 LYS Chi-restraints excluded: chain R residue 292 SER Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 335 ILE Chi-restraints excluded: chain R residue 341 HIS Chi-restraints excluded: chain R residue 370 PHE Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 33 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 158 HIS R 341 HIS A 213 GLN B 13 GLN N 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.122490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.087316 restraints weight = 13401.700| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.21 r_work: 0.2938 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8143 Z= 0.153 Angle : 0.599 8.960 11041 Z= 0.312 Chirality : 0.043 0.181 1231 Planarity : 0.004 0.041 1400 Dihedral : 12.463 130.323 1153 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.91 % Allowed : 29.47 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.27), residues: 983 helix: 1.99 (0.27), residues: 359 sheet: 0.63 (0.34), residues: 220 loop : -0.42 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 27 TYR 0.015 0.001 TYR N 60 PHE 0.020 0.001 PHE N 108 TRP 0.019 0.001 TRP N 47 HIS 0.002 0.001 HIS R 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 8141) covalent geometry : angle 0.59880 / 0.31 (11039) SS BOND : bond 0.00188 / 0.10 ( 1) SS BOND : angle 0.71961 / 0.38 ( 2) hydrogen bonds : bond 0.03935 / 2.54 ( 385) hydrogen bonds : angle 3.96902 / 2.90 ( 1083) Misc. bond : bond 0.00229 / 0.12 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 182 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7807 (mmmm) REVERT: R 183 ASP cc_start: 0.8274 (m-30) cc_final: 0.8013 (m-30) REVERT: A 15 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8408 (mm-30) REVERT: A 16 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: A 20 ARG cc_start: 0.7928 (tpt-90) cc_final: 0.7598 (tpt90) REVERT: A 213 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8566 (tt0) REVERT: A 280 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8444 (tttm) REVERT: A 283 ARG cc_start: 0.8149 (ptp-170) cc_final: 0.7895 (ptp-110) REVERT: A 339 TYR cc_start: 0.8271 (m-80) cc_final: 0.7740 (m-80) REVERT: B 32 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7553 (mp10) REVERT: B 132 ASN cc_start: 0.8562 (m110) cc_final: 0.8240 (p0) REVERT: B 138 GLU cc_start: 0.8808 (tp30) cc_final: 0.8560 (mm-30) REVERT: B 153 ASP cc_start: 0.8539 (m-30) cc_final: 0.7842 (p0) REVERT: B 175 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7793 (pp30) REVERT: B 217 MET cc_start: 0.8510 (pmm) cc_final: 0.8045 (pmm) REVERT: B 234 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8338 (t80) REVERT: B 260 GLU cc_start: 0.8429 (pt0) cc_final: 0.7744 (tt0) REVERT: B 262 MET cc_start: 0.8408 (tpp) cc_final: 0.7764 (tpp) REVERT: G 14 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8698 (mmtm) REVERT: G 21 MET cc_start: 0.8462 (ttp) cc_final: 0.8036 (ttt) REVERT: G 46 LYS cc_start: 0.9012 (tptp) cc_final: 0.8382 (tptp) REVERT: G 47 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8190 (mm-30) REVERT: N 28 THR cc_start: 0.8326 (m) cc_final: 0.7822 (p) REVERT: N 33 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6717 (ttmt) REVERT: N 38 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7679 (ttp80) REVERT: N 53 GLN cc_start: 0.8611 (mp10) cc_final: 0.8406 (mp10) outliers start: 42 outliers final: 23 residues processed: 181 average time/residue: 0.4677 time to fit residues: 90.2350 Evaluate side-chains 186 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 TYR Chi-restraints excluded: chain R residue 145 PHE Chi-restraints excluded: chain R residue 159 CYS Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 182 LYS Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 292 SER Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 335 ILE Chi-restraints excluded: chain R residue 341 HIS Chi-restraints excluded: chain R residue 370 PHE Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 9 optimal weight: 0.0970 chunk 51 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 158 HIS ** R 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN B 9 GLN B 13 GLN N 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.124236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.089812 restraints weight = 13447.661| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.15 r_work: 0.2986 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8143 Z= 0.133 Angle : 0.600 9.345 11041 Z= 0.313 Chirality : 0.043 0.206 1231 Planarity : 0.004 0.041 1400 Dihedral : 12.437 130.480 1153 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.56 % Allowed : 29.82 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.27), residues: 983 helix: 1.99 (0.27), residues: 359 sheet: 0.63 (0.34), residues: 221 loop : -0.37 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 27 TYR 0.016 0.001 TYR N 60 PHE 0.018 0.001 PHE N 27 TRP 0.030 0.002 TRP N 47 HIS 0.013 0.001 HIS R 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 8141) covalent geometry : angle 0.59953 / 0.31 (11039) SS BOND : bond 0.00154 / 0.08 ( 1) SS BOND : angle 0.62930 / 0.34 ( 2) hydrogen bonds : bond 0.03804 / 2.46 ( 385) hydrogen bonds : angle 3.94673 / 2.89 ( 1083) Misc. bond : bond 0.00102 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 182 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7765 (mmmm) REVERT: R 183 ASP cc_start: 0.8285 (m-30) cc_final: 0.8025 (m-30) REVERT: A 15 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8392 (mm-30) REVERT: A 16 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: A 213 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8598 (tt0) REVERT: A 280 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8409 (tttm) REVERT: A 283 ARG cc_start: 0.8009 (ptp-170) cc_final: 0.7748 (ptp-110) REVERT: A 339 TYR cc_start: 0.8118 (m-80) cc_final: 0.7598 (m-80) REVERT: B 9 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8654 (mm110) REVERT: B 32 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7467 (mp10) REVERT: B 138 GLU cc_start: 0.8847 (tp30) cc_final: 0.8595 (mm-30) REVERT: B 153 ASP cc_start: 0.8502 (m-30) cc_final: 0.7797 (p0) REVERT: B 175 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7649 (pp30) REVERT: B 217 MET cc_start: 0.8424 (pmm) cc_final: 0.7956 (pmm) REVERT: B 234 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8226 (t80) REVERT: B 260 GLU cc_start: 0.8408 (pt0) cc_final: 0.7783 (tt0) REVERT: B 262 MET cc_start: 0.8352 (tpp) cc_final: 0.7640 (tpp) REVERT: G 17 GLU cc_start: 0.8646 (tp30) cc_final: 0.8384 (tp30) REVERT: G 21 MET cc_start: 0.8443 (ttp) cc_final: 0.7865 (ttt) REVERT: G 46 LYS cc_start: 0.9024 (tptp) cc_final: 0.8344 (tptp) REVERT: G 47 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8150 (mm-30) REVERT: N 28 THR cc_start: 0.8192 (m) cc_final: 0.7663 (p) REVERT: N 33 LYS cc_start: 0.6630 (OUTLIER) cc_final: 0.6317 (ttmt) REVERT: N 38 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7453 (ttp80) REVERT: N 53 GLN cc_start: 0.8502 (mp10) cc_final: 0.8292 (mp10) outliers start: 39 outliers final: 23 residues processed: 180 average time/residue: 0.5372 time to fit residues: 102.8423 Evaluate side-chains 183 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 TYR Chi-restraints excluded: chain R residue 145 PHE Chi-restraints excluded: chain R residue 159 CYS Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 182 LYS Chi-restraints excluded: chain R residue 292 SER Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 335 ILE Chi-restraints excluded: chain R residue 341 HIS Chi-restraints excluded: chain R residue 370 PHE Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 158 HIS ** R 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 341 HIS ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN B 13 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.124492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.088653 restraints weight = 13289.303| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.23 r_work: 0.2996 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8143 Z= 0.139 Angle : 0.625 9.876 11041 Z= 0.321 Chirality : 0.043 0.200 1231 Planarity : 0.004 0.043 1400 Dihedral : 12.809 130.756 1153 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.91 % Allowed : 30.41 % Favored : 64.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.27), residues: 983 helix: 2.03 (0.27), residues: 357 sheet: 0.67 (0.34), residues: 221 loop : -0.33 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 19 TYR 0.016 0.001 TYR N 60 PHE 0.022 0.001 PHE N 108 TRP 0.031 0.002 TRP N 47 HIS 0.002 0.000 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 8141) covalent geometry : angle 0.62527 / 0.32 (11039) SS BOND : bond 0.00174 / 0.09 ( 1) SS BOND : angle 0.61784 / 0.33 ( 2) hydrogen bonds : bond 0.03839 / 2.48 ( 385) hydrogen bonds : angle 3.95417 / 2.90 ( 1083) Misc. bond : bond 0.00642 / 0.34 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 182 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7809 (mmmm) REVERT: R 183 ASP cc_start: 0.8294 (m-30) cc_final: 0.8033 (m-30) REVERT: R 381 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8547 (mm110) REVERT: A 15 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8384 (mm-30) REVERT: A 16 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: A 213 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8555 (tt0) REVERT: A 280 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8405 (tttm) REVERT: A 283 ARG cc_start: 0.8109 (ptp-170) cc_final: 0.7842 (ptp-110) REVERT: A 339 TYR cc_start: 0.8083 (m-80) cc_final: 0.7599 (m-80) REVERT: B 32 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7434 (mp10) REVERT: B 138 GLU cc_start: 0.8847 (tp30) cc_final: 0.8615 (mm-30) REVERT: B 153 ASP cc_start: 0.8484 (m-30) cc_final: 0.7800 (p0) REVERT: B 175 GLN cc_start: 0.7994 (tm-30) cc_final: 0.7609 (pp30) REVERT: B 217 MET cc_start: 0.8411 (pmm) cc_final: 0.7929 (pmm) REVERT: B 234 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8231 (t80) REVERT: B 260 GLU cc_start: 0.8394 (pt0) cc_final: 0.7780 (tt0) REVERT: B 262 MET cc_start: 0.8354 (tpp) cc_final: 0.7656 (tpp) REVERT: G 17 GLU cc_start: 0.8624 (tp30) cc_final: 0.8383 (tp30) REVERT: G 21 MET cc_start: 0.8405 (ttp) cc_final: 0.7813 (ttt) REVERT: G 46 LYS cc_start: 0.9045 (tptp) cc_final: 0.8361 (tptp) REVERT: G 47 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8154 (mm-30) REVERT: N 33 LYS cc_start: 0.6598 (OUTLIER) cc_final: 0.6343 (ttmt) REVERT: N 38 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7482 (ttp80) REVERT: N 53 GLN cc_start: 0.8481 (mp10) cc_final: 0.8271 (mp10) REVERT: N 82 GLN cc_start: 0.6616 (OUTLIER) cc_final: 0.6248 (tp40) outliers start: 42 outliers final: 23 residues processed: 174 average time/residue: 0.5367 time to fit residues: 99.3230 Evaluate side-chains 180 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 TYR Chi-restraints excluded: chain R residue 145 PHE Chi-restraints excluded: chain R residue 159 CYS Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 182 LYS Chi-restraints excluded: chain R residue 292 SER Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 335 ILE Chi-restraints excluded: chain R residue 341 HIS Chi-restraints excluded: chain R residue 381 GLN Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 35 optimal weight: 0.0010 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 93 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 90 optimal weight: 0.0970 chunk 46 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.2980 chunk 41 optimal weight: 0.9980 overall best weight: 0.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 158 HIS ** R 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 341 HIS ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.126629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.091291 restraints weight = 13315.509| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.25 r_work: 0.3020 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8143 Z= 0.124 Angle : 0.647 10.829 11041 Z= 0.331 Chirality : 0.043 0.197 1231 Planarity : 0.004 0.040 1400 Dihedral : 12.728 131.879 1151 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.16 % Allowed : 32.16 % Favored : 64.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.27), residues: 983 helix: 2.19 (0.27), residues: 351 sheet: 0.77 (0.34), residues: 220 loop : -0.36 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 19 TYR 0.017 0.001 TYR N 60 PHE 0.020 0.001 PHE N 27 TRP 0.033 0.002 TRP N 47 HIS 0.003 0.001 HIS R 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 8141) covalent geometry : angle 0.64695 / 0.33 (11039) SS BOND : bond 0.00126 / 0.07 ( 1) SS BOND : angle 0.53024 / 0.29 ( 2) hydrogen bonds : bond 0.03691 / 2.40 ( 385) hydrogen bonds : angle 3.92993 / 2.88 ( 1083) Misc. bond : bond 0.00578 / 0.30 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 182 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7802 (mmmm) REVERT: R 183 ASP cc_start: 0.8310 (m-30) cc_final: 0.8058 (m-30) REVERT: A 15 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8353 (mm-30) REVERT: A 16 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: A 213 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8590 (tt0) REVERT: A 280 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8379 (tttm) REVERT: A 283 ARG cc_start: 0.7985 (ptp-170) cc_final: 0.7726 (ptp-110) REVERT: A 339 TYR cc_start: 0.7911 (m-80) cc_final: 0.7466 (m-80) REVERT: B 32 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7380 (mp10) REVERT: B 138 GLU cc_start: 0.8879 (tp30) cc_final: 0.8595 (mm-30) REVERT: B 153 ASP cc_start: 0.8416 (m-30) cc_final: 0.7717 (p0) REVERT: B 175 GLN cc_start: 0.7988 (tm-30) cc_final: 0.7577 (pp30) REVERT: B 217 MET cc_start: 0.8384 (pmm) cc_final: 0.7917 (pmm) REVERT: B 234 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8270 (t80) REVERT: B 260 GLU cc_start: 0.8367 (pt0) cc_final: 0.7768 (tt0) REVERT: B 262 MET cc_start: 0.8344 (tpp) cc_final: 0.7633 (tpp) REVERT: G 17 GLU cc_start: 0.8606 (tp30) cc_final: 0.8380 (tp30) REVERT: G 21 MET cc_start: 0.8409 (ttp) cc_final: 0.7816 (ttt) REVERT: G 46 LYS cc_start: 0.9039 (tptp) cc_final: 0.8344 (tptp) REVERT: G 47 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8132 (mm-30) REVERT: N 38 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7469 (ttp80) REVERT: N 53 GLN cc_start: 0.8450 (mp10) cc_final: 0.8232 (mp10) outliers start: 27 outliers final: 15 residues processed: 169 average time/residue: 0.5352 time to fit residues: 96.2846 Evaluate side-chains 168 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 TYR Chi-restraints excluded: chain R residue 145 PHE Chi-restraints excluded: chain R residue 159 CYS Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 182 LYS Chi-restraints excluded: chain R residue 292 SER Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 335 ILE Chi-restraints excluded: chain R residue 341 HIS Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 24 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 158 HIS ** R 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 341 HIS ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN B 9 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN N 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.125395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.089915 restraints weight = 13293.279| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.22 r_work: 0.3001 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8143 Z= 0.148 Angle : 0.666 11.748 11041 Z= 0.339 Chirality : 0.043 0.190 1231 Planarity : 0.004 0.040 1400 Dihedral : 12.582 133.340 1149 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.51 % Allowed : 32.16 % Favored : 64.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.27), residues: 983 helix: 2.00 (0.27), residues: 357 sheet: 0.77 (0.34), residues: 220 loop : -0.32 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 19 TYR 0.023 0.001 TYR N 117 PHE 0.024 0.002 PHE N 27 TRP 0.032 0.002 TRP N 47 HIS 0.006 0.001 HIS R 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 8141) covalent geometry : angle 0.66569 / 0.34 (11039) SS BOND : bond 0.00192 / 0.10 ( 1) SS BOND : angle 0.62744 / 0.33 ( 2) hydrogen bonds : bond 0.03863 / 2.51 ( 385) hydrogen bonds : angle 3.98033 / 2.91 ( 1083) Misc. bond : bond 0.00666 / 0.35 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2897.00 seconds wall clock time: 50 minutes 7.94 seconds (3007.94 seconds total)