Starting phenix.real_space_refine on Sat Aug 23 01:23:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wwn_37894/08_2025/8wwn_37894.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wwn_37894/08_2025/8wwn_37894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wwn_37894/08_2025/8wwn_37894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wwn_37894/08_2025/8wwn_37894.map" model { file = "/net/cci-nas-00/data/ceres_data/8wwn_37894/08_2025/8wwn_37894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wwn_37894/08_2025/8wwn_37894.cif" } resolution = 2.65 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= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 5705 2.51 5 N 1517 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8960 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1749 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" 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: "E" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1779 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2235 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 15, 'TRANS': 273} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "L" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 139 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 15} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 1.72, per 1000 atoms: 0.19 Number of scatterers: 8960 At special positions: 0 Unit cell: (87.74, 116.63, 125.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 1670 8.00 N 1517 7.00 C 5705 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 185 " - pdb=" SG CYS R 263 " distance=2.03 Simple disulfide: pdb=" SG CYS L 7 " - pdb=" SG CYS L 16 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 291.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 15 sheets defined 37.8% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.559A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.525A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.346A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.900A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.027A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.130A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'R' and resid 108 through 138 Proline residue: R 113 - end of helix Processing helix chain 'R' and resid 145 through 164 Processing helix chain 'R' and resid 165 through 174 removed outlier: 6.120A pdb=" N GLN R 171 " --> pdb=" O PHE R 167 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU R 172 " --> pdb=" O MET R 168 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET R 173 " --> pdb=" O ILE R 169 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY R 174 " --> pdb=" O HIS R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 216 removed outlier: 3.779A pdb=" N MET R 184 " --> pdb=" O PHE R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 223 removed outlier: 3.681A pdb=" N LYS R 222 " --> pdb=" O SER R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 244 Processing helix chain 'R' and resid 244 through 250 removed outlier: 3.569A pdb=" N TYR R 250 " --> pdb=" O PRO R 246 " (cutoff:3.500A) Processing helix chain 'R' and resid 273 through 286 Processing helix chain 'R' and resid 286 through 303 Processing helix chain 'R' and resid 313 through 348 Proline residue: R 340 - end of helix Processing helix chain 'R' and resid 355 through 384 removed outlier: 4.202A pdb=" N SER R 373 " --> pdb=" O GLY R 369 " (cutoff:3.500A) Proline residue: R 377 - end of helix removed outlier: 3.524A pdb=" N CYS R 384 " --> pdb=" O TYR R 380 " (cutoff:3.500A) Processing helix chain 'R' and resid 384 through 395 removed outlier: 3.501A pdb=" N SER R 394 " --> pdb=" O ARG R 390 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.310A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.698A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.544A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.905A 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: 5.947A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.627A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.870A 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: 6.683A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.385A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.679A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.714A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.240A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.443A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 251 through 255 Processing sheet with id=AB6, first strand: chain 'L' and resid 8 through 9 removed outlier: 3.663A pdb=" N VAL L 12 " --> pdb=" O LEU L 9 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1311 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: 1.01 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2890 1.34 - 1.46: 2125 1.46 - 1.58: 4037 1.58 - 1.69: 0 1.69 - 1.81: 99 Bond restraints: 9151 Sorted by residual: bond pdb=" CG1 ILE B 273 " pdb=" CD1 ILE B 273 " ideal model delta sigma weight residual 1.513 1.486 0.027 3.90e-02 6.57e+02 4.67e-01 bond pdb=" C ALA E 241 " pdb=" N GLY E 242 " ideal model delta sigma weight residual 1.331 1.321 0.010 1.46e-02 4.69e+03 4.65e-01 bond pdb=" CA PRO R 310 " pdb=" C PRO R 310 " ideal model delta sigma weight residual 1.527 1.520 0.007 1.07e-02 8.73e+03 4.53e-01 bond pdb=" C LEU A 39 " pdb=" N GLY A 40 " ideal model delta sigma weight residual 1.331 1.321 0.009 1.46e-02 4.69e+03 3.93e-01 bond pdb=" CG PRO R 217 " pdb=" CD PRO R 217 " ideal model delta sigma weight residual 1.503 1.482 0.021 3.40e-02 8.65e+02 3.67e-01 ... (remaining 9146 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 12098 1.09 - 2.18: 254 2.18 - 3.28: 50 3.28 - 4.37: 7 4.37 - 5.46: 11 Bond angle restraints: 12420 Sorted by residual: angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.20 110.08 3.12 9.60e-01 1.09e+00 1.05e+01 angle pdb=" C ASN R 145 " pdb=" N VAL R 146 " pdb=" CA VAL R 146 " ideal model delta sigma weight residual 120.33 122.64 -2.31 8.00e-01 1.56e+00 8.33e+00 angle pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 122.74 125.99 -3.25 1.44e+00 4.82e-01 5.08e+00 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 125.71 -4.17 1.91e+00 2.74e-01 4.77e+00 angle pdb=" C VAL R 146 " pdb=" CA VAL R 146 " pdb=" CB VAL R 146 " ideal model delta sigma weight residual 114.00 111.23 2.77 1.31e+00 5.83e-01 4.48e+00 ... (remaining 12415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5236 17.93 - 35.86: 152 35.86 - 53.80: 30 53.80 - 71.73: 2 71.73 - 89.66: 2 Dihedral angle restraints: 5422 sinusoidal: 2056 harmonic: 3366 Sorted by residual: dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 162.41 17.59 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 163.00 17.00 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 163.56 16.44 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 5419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 859 0.028 - 0.055: 362 0.055 - 0.083: 112 0.083 - 0.110: 74 0.110 - 0.138: 18 Chirality restraints: 1425 Sorted by residual: chirality pdb=" CA ILE E 189 " pdb=" N ILE E 189 " pdb=" C ILE E 189 " pdb=" CB ILE E 189 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CA PRO B 236 " pdb=" N PRO B 236 " pdb=" C PRO B 236 " pdb=" CB PRO B 236 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 1422 not shown) Planarity restraints: 1571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO B 236 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 106 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.74e+00 pdb=" N PRO E 107 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO E 107 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 107 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " -0.020 5.00e-02 4.00e+02 2.95e-02 1.40e+00 pdb=" N PRO B 194 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.017 5.00e-02 4.00e+02 ... (remaining 1568 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 383 2.72 - 3.27: 8868 3.27 - 3.81: 15152 3.81 - 4.36: 19541 4.36 - 4.90: 33044 Nonbonded interactions: 76988 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 175 " model vdw 2.180 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.211 3.040 nonbonded pdb=" O SER R 243 " pdb=" OH TYR R 280 " model vdw 2.270 3.040 nonbonded pdb=" O GLN R 171 " pdb=" OH TYR L 13 " model vdw 2.288 3.040 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.289 3.040 ... (remaining 76983 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.910 Find NCS groups from input model: 0.030 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:8.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 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 : 0.002 0.027 9155 Z= 0.103 Angle : 0.443 5.461 12428 Z= 0.245 Chirality : 0.040 0.138 1425 Planarity : 0.003 0.053 1571 Dihedral : 9.194 89.661 3238 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.62 % Allowed : 4.34 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 0.87 (0.25), residues: 1144 helix: 0.79 (0.25), residues: 393 sheet: 0.74 (0.29), residues: 298 loop : 0.48 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 38 TYR 0.009 0.001 TYR E 103 PHE 0.016 0.001 PHE B 151 TRP 0.010 0.001 TRP B 339 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 9151) covalent geometry : angle 0.44238 (12420) SS BOND : bond 0.00196 ( 4) SS BOND : angle 0.62414 ( 8) hydrogen bonds : bond 0.23265 ( 467) hydrogen bonds : angle 7.20594 ( 1311) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 184 time to evaluate : 0.365 Fit side-chains REVERT: A 21 ARG cc_start: 0.8125 (ttm170) cc_final: 0.7882 (ttm170) REVERT: A 22 ASN cc_start: 0.8404 (m-40) cc_final: 0.8174 (m110) REVERT: A 24 ARG cc_start: 0.7909 (ttm110) cc_final: 0.7444 (mtm110) REVERT: A 208 ARG cc_start: 0.7964 (ttm-80) cc_final: 0.7600 (ttm110) REVERT: A 312 LYS cc_start: 0.8286 (tppt) cc_final: 0.8071 (mptt) REVERT: B 25 CYS cc_start: 0.8459 (p) cc_final: 0.8221 (p) REVERT: B 124 TYR cc_start: 0.9084 (m-80) cc_final: 0.8814 (m-80) REVERT: B 137 ARG cc_start: 0.8409 (mmt-90) cc_final: 0.8103 (mmt90) REVERT: B 138 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8413 (mt-10) REVERT: E 30 SER cc_start: 0.8794 (p) cc_final: 0.8571 (m) REVERT: E 46 GLU cc_start: 0.8234 (tt0) cc_final: 0.8030 (tt0) REVERT: R 239 LEU cc_start: 0.7679 (mt) cc_final: 0.7350 (tp) REVERT: R 266 ARG cc_start: 0.7632 (mtp180) cc_final: 0.7237 (mtm110) REVERT: R 325 ARG cc_start: 0.7348 (ptt-90) cc_final: 0.6865 (ptt-90) outliers start: 6 outliers final: 3 residues processed: 188 average time/residue: 0.5465 time to fit residues: 108.6822 Evaluate side-chains 153 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 150 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain R residue 280 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN A 322 HIS A 333 GLN B 220 GLN E 3 GLN R 281 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.172838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.137191 restraints weight = 9118.606| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.61 r_work: 0.3307 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9155 Z= 0.149 Angle : 0.537 6.242 12428 Z= 0.292 Chirality : 0.043 0.150 1425 Planarity : 0.004 0.054 1571 Dihedral : 4.908 55.503 1257 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.90 % Allowed : 9.72 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 1.41 (0.25), residues: 1144 helix: 2.01 (0.26), residues: 397 sheet: 0.67 (0.29), residues: 301 loop : 0.24 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 251 TYR 0.013 0.001 TYR A 320 PHE 0.017 0.002 PHE B 151 TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9151) covalent geometry : angle 0.53685 (12420) SS BOND : bond 0.00280 ( 4) SS BOND : angle 0.56985 ( 8) hydrogen bonds : bond 0.05506 ( 467) hydrogen bonds : angle 5.12228 ( 1311) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8340 (ttm170) cc_final: 0.8114 (ttp-110) REVERT: A 22 ASN cc_start: 0.8355 (m-40) cc_final: 0.8046 (m-40) REVERT: A 24 ARG cc_start: 0.8001 (ttm110) cc_final: 0.7408 (mtt90) REVERT: A 25 GLU cc_start: 0.7847 (tt0) cc_final: 0.7623 (mt-10) REVERT: A 46 LYS cc_start: 0.7544 (ttpm) cc_final: 0.7044 (ttpt) REVERT: A 208 ARG cc_start: 0.8064 (ttm-80) cc_final: 0.7495 (ttm110) REVERT: A 305 CYS cc_start: 0.8409 (m) cc_final: 0.7949 (t) REVERT: A 312 LYS cc_start: 0.8381 (tppt) cc_final: 0.8120 (mptt) REVERT: B 124 TYR cc_start: 0.8974 (m-80) cc_final: 0.8723 (m-80) REVERT: B 197 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7525 (mtt-85) REVERT: C 21 MET cc_start: 0.7749 (mmm) cc_final: 0.6826 (tmm) REVERT: R 165 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7642 (ttt) REVERT: R 235 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7778 (tt) REVERT: R 239 LEU cc_start: 0.7223 (mt) cc_final: 0.6777 (tp) REVERT: R 266 ARG cc_start: 0.7642 (mtp180) cc_final: 0.7101 (mtm110) REVERT: R 359 VAL cc_start: 0.8045 (t) cc_final: 0.7812 (m) outliers start: 28 outliers final: 11 residues processed: 164 average time/residue: 0.5454 time to fit residues: 94.5954 Evaluate side-chains 160 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain L residue 8 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 59 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 31 optimal weight: 0.0470 chunk 21 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 304 GLN B 259 GLN E 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.173976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.138716 restraints weight = 9151.705| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.60 r_work: 0.3336 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9155 Z= 0.118 Angle : 0.484 5.134 12428 Z= 0.263 Chirality : 0.041 0.149 1425 Planarity : 0.004 0.053 1571 Dihedral : 4.342 50.306 1255 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.41 % Allowed : 10.65 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 1.55 (0.25), residues: 1144 helix: 2.41 (0.26), residues: 397 sheet: 0.54 (0.29), residues: 304 loop : 0.20 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 251 TYR 0.012 0.001 TYR E 190 PHE 0.015 0.001 PHE B 151 TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9151) covalent geometry : angle 0.48349 (12420) SS BOND : bond 0.00259 ( 4) SS BOND : angle 0.63018 ( 8) hydrogen bonds : bond 0.04358 ( 467) hydrogen bonds : angle 4.70564 ( 1311) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8304 (m-40) cc_final: 0.8053 (m-40) REVERT: A 24 ARG cc_start: 0.7898 (ttm110) cc_final: 0.7376 (mtm110) REVERT: A 25 GLU cc_start: 0.7759 (tt0) cc_final: 0.7554 (mt-10) REVERT: A 208 ARG cc_start: 0.8004 (ttm-80) cc_final: 0.7451 (ttm110) REVERT: A 304 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.8038 (tm-30) REVERT: A 305 CYS cc_start: 0.8354 (m) cc_final: 0.7961 (t) REVERT: A 312 LYS cc_start: 0.8318 (tppt) cc_final: 0.8113 (mptt) REVERT: B 129 ARG cc_start: 0.8240 (mtp180) cc_final: 0.8009 (tpt90) REVERT: B 217 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.7609 (pmt) REVERT: C 21 MET cc_start: 0.7852 (mmm) cc_final: 0.6808 (tmm) REVERT: R 165 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7778 (ttt) REVERT: R 235 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7805 (tt) REVERT: R 239 LEU cc_start: 0.7195 (mt) cc_final: 0.6755 (tp) REVERT: R 252 ARG cc_start: 0.6658 (OUTLIER) cc_final: 0.5849 (mpp80) REVERT: R 266 ARG cc_start: 0.7671 (mtp180) cc_final: 0.6974 (mtm110) outliers start: 33 outliers final: 11 residues processed: 170 average time/residue: 0.5740 time to fit residues: 103.2868 Evaluate side-chains 156 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain L residue 8 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 79 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 99 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 112 optimal weight: 0.0970 chunk 2 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.173391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.137772 restraints weight = 9289.470| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.61 r_work: 0.3321 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9155 Z= 0.127 Angle : 0.486 5.140 12428 Z= 0.264 Chirality : 0.042 0.146 1425 Planarity : 0.004 0.053 1571 Dihedral : 4.298 50.841 1254 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.62 % Allowed : 11.38 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 1.54 (0.25), residues: 1144 helix: 2.55 (0.26), residues: 389 sheet: 0.43 (0.29), residues: 302 loop : 0.16 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 251 TYR 0.013 0.001 TYR R 342 PHE 0.016 0.001 PHE B 151 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9151) covalent geometry : angle 0.48581 (12420) SS BOND : bond 0.00248 ( 4) SS BOND : angle 0.60513 ( 8) hydrogen bonds : bond 0.04185 ( 467) hydrogen bonds : angle 4.64861 ( 1311) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.391 Fit side-chains REVERT: A 24 ARG cc_start: 0.7915 (ttm110) cc_final: 0.7583 (mtm-85) REVERT: A 25 GLU cc_start: 0.7845 (tt0) cc_final: 0.7611 (mt-10) REVERT: A 208 ARG cc_start: 0.7968 (ttm-80) cc_final: 0.7425 (ttm110) REVERT: A 209 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7856 (ptmm) REVERT: A 305 CYS cc_start: 0.8307 (m) cc_final: 0.7815 (t) REVERT: B 129 ARG cc_start: 0.8236 (mtp180) cc_final: 0.8005 (tpt90) REVERT: C 21 MET cc_start: 0.7868 (mmm) cc_final: 0.6793 (tmm) REVERT: R 165 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7911 (ttt) REVERT: R 235 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7859 (tt) REVERT: R 239 LEU cc_start: 0.7128 (mt) cc_final: 0.6676 (tp) REVERT: R 252 ARG cc_start: 0.6704 (OUTLIER) cc_final: 0.5696 (mpp80) REVERT: R 283 PHE cc_start: 0.8057 (t80) cc_final: 0.6270 (m-10) outliers start: 35 outliers final: 18 residues processed: 163 average time/residue: 0.6925 time to fit residues: 119.1291 Evaluate side-chains 164 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 192 ASP Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 304 MET Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain L residue 8 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 28 optimal weight: 0.3980 chunk 81 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.171797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.136992 restraints weight = 9176.396| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.70 r_work: 0.3294 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9155 Z= 0.159 Angle : 0.520 5.701 12428 Z= 0.281 Chirality : 0.043 0.148 1425 Planarity : 0.004 0.056 1571 Dihedral : 4.483 51.695 1254 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.83 % Allowed : 11.69 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 1.41 (0.25), residues: 1144 helix: 2.51 (0.26), residues: 390 sheet: 0.35 (0.29), residues: 301 loop : 0.02 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 251 TYR 0.015 0.002 TYR E 103 PHE 0.019 0.002 PHE B 151 TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9151) covalent geometry : angle 0.51953 (12420) SS BOND : bond 0.00294 ( 4) SS BOND : angle 0.64827 ( 8) hydrogen bonds : bond 0.04386 ( 467) hydrogen bonds : angle 4.74301 ( 1311) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 0.357 Fit side-chains REVERT: A 24 ARG cc_start: 0.7934 (ttm110) cc_final: 0.7641 (mtm-85) REVERT: A 25 GLU cc_start: 0.7824 (tt0) cc_final: 0.7586 (mt-10) REVERT: A 208 ARG cc_start: 0.7966 (ttm-80) cc_final: 0.7386 (ttm110) REVERT: A 209 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7982 (ptmm) REVERT: A 305 CYS cc_start: 0.8414 (m) cc_final: 0.7915 (t) REVERT: B 129 ARG cc_start: 0.8241 (mtp180) cc_final: 0.7999 (tpt90) REVERT: B 134 ARG cc_start: 0.8646 (ptt-90) cc_final: 0.8426 (ptt-90) REVERT: B 217 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.7846 (pmt) REVERT: C 21 MET cc_start: 0.7859 (mmm) cc_final: 0.6679 (tmm) REVERT: R 165 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7920 (ttt) REVERT: R 235 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7888 (tt) REVERT: R 239 LEU cc_start: 0.7216 (mt) cc_final: 0.6732 (tp) REVERT: R 252 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.5708 (mpp80) REVERT: R 283 PHE cc_start: 0.8028 (t80) cc_final: 0.6288 (m-10) outliers start: 37 outliers final: 21 residues processed: 163 average time/residue: 0.6506 time to fit residues: 112.2255 Evaluate side-chains 165 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 192 ASP Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 304 MET Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain L residue 8 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 43 optimal weight: 0.0570 chunk 35 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.173035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.137754 restraints weight = 9147.439| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.63 r_work: 0.3325 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9155 Z= 0.126 Angle : 0.487 5.285 12428 Z= 0.263 Chirality : 0.042 0.145 1425 Planarity : 0.004 0.056 1571 Dihedral : 4.375 51.787 1254 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.62 % Allowed : 12.51 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 1.42 (0.25), residues: 1144 helix: 2.59 (0.26), residues: 390 sheet: 0.30 (0.29), residues: 303 loop : 0.01 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 251 TYR 0.012 0.001 TYR R 342 PHE 0.017 0.001 PHE B 151 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9151) covalent geometry : angle 0.48660 (12420) SS BOND : bond 0.00246 ( 4) SS BOND : angle 0.52651 ( 8) hydrogen bonds : bond 0.04012 ( 467) hydrogen bonds : angle 4.59837 ( 1311) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.326 Fit side-chains REVERT: A 24 ARG cc_start: 0.7947 (ttm110) cc_final: 0.7426 (mtm110) REVERT: A 25 GLU cc_start: 0.7772 (tt0) cc_final: 0.7563 (mt-10) REVERT: A 208 ARG cc_start: 0.7971 (ttm-80) cc_final: 0.7414 (ttm110) REVERT: A 209 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7961 (ptmm) REVERT: A 305 CYS cc_start: 0.8365 (m) cc_final: 0.7935 (t) REVERT: B 129 ARG cc_start: 0.8236 (mtp180) cc_final: 0.8013 (tpt90) REVERT: B 217 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.7773 (pmt) REVERT: C 21 MET cc_start: 0.7863 (mmm) cc_final: 0.6690 (tmm) REVERT: R 165 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7968 (ttt) REVERT: R 235 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7888 (tp) REVERT: R 239 LEU cc_start: 0.7203 (mt) cc_final: 0.6740 (tp) REVERT: R 252 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.5721 (mpp80) REVERT: R 283 PHE cc_start: 0.8021 (t80) cc_final: 0.6356 (m-10) outliers start: 35 outliers final: 18 residues processed: 157 average time/residue: 0.6972 time to fit residues: 115.3744 Evaluate side-chains 159 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 192 ASP Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 304 MET Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain L residue 8 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 84 optimal weight: 0.0270 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.172876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.136987 restraints weight = 9189.181| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.61 r_work: 0.3309 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9155 Z= 0.129 Angle : 0.493 6.716 12428 Z= 0.265 Chirality : 0.042 0.145 1425 Planarity : 0.004 0.055 1571 Dihedral : 4.381 52.016 1254 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.52 % Allowed : 12.62 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 1.42 (0.25), residues: 1144 helix: 2.63 (0.26), residues: 390 sheet: 0.28 (0.28), residues: 303 loop : -0.02 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 251 TYR 0.013 0.001 TYR R 342 PHE 0.016 0.001 PHE B 151 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9151) covalent geometry : angle 0.49263 (12420) SS BOND : bond 0.00222 ( 4) SS BOND : angle 0.55401 ( 8) hydrogen bonds : bond 0.03991 ( 467) hydrogen bonds : angle 4.59028 ( 1311) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7915 (ttm110) cc_final: 0.7403 (mtm110) REVERT: A 25 GLU cc_start: 0.7794 (tt0) cc_final: 0.7573 (mt-10) REVERT: A 208 ARG cc_start: 0.7927 (ttm-80) cc_final: 0.7367 (ttm110) REVERT: A 209 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.8002 (ptmm) REVERT: A 305 CYS cc_start: 0.8383 (m) cc_final: 0.7942 (t) REVERT: B 129 ARG cc_start: 0.8318 (mtp180) cc_final: 0.8014 (tpt90) REVERT: B 134 ARG cc_start: 0.8644 (ptt-90) cc_final: 0.8432 (ptt-90) REVERT: B 217 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.7780 (pmt) REVERT: C 21 MET cc_start: 0.7892 (mmm) cc_final: 0.6710 (tmm) REVERT: R 165 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7942 (ttt) REVERT: R 235 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7875 (tp) REVERT: R 239 LEU cc_start: 0.7201 (mt) cc_final: 0.6735 (tp) REVERT: R 252 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.5736 (mpp80) REVERT: R 283 PHE cc_start: 0.7984 (t80) cc_final: 0.6339 (m-10) outliers start: 34 outliers final: 20 residues processed: 154 average time/residue: 0.6250 time to fit residues: 101.6877 Evaluate side-chains 160 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 192 ASP Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 304 MET Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 386 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 3 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.172327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.136582 restraints weight = 9223.961| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.62 r_work: 0.3288 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9155 Z= 0.143 Angle : 0.506 6.821 12428 Z= 0.272 Chirality : 0.042 0.145 1425 Planarity : 0.004 0.056 1571 Dihedral : 4.447 52.108 1254 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.72 % Allowed : 12.20 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 1.39 (0.25), residues: 1144 helix: 2.63 (0.26), residues: 389 sheet: 0.23 (0.28), residues: 303 loop : -0.05 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 251 TYR 0.014 0.002 TYR E 103 PHE 0.017 0.001 PHE B 151 TRP 0.015 0.002 TRP R 248 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9151) covalent geometry : angle 0.50623 (12420) SS BOND : bond 0.00227 ( 4) SS BOND : angle 0.54965 ( 8) hydrogen bonds : bond 0.04106 ( 467) hydrogen bonds : angle 4.63499 ( 1311) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7947 (ttm110) cc_final: 0.7670 (mtm-85) REVERT: A 25 GLU cc_start: 0.7831 (tt0) cc_final: 0.7584 (mt-10) REVERT: A 208 ARG cc_start: 0.7958 (ttm-80) cc_final: 0.7381 (ttm110) REVERT: A 209 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8056 (ptmm) REVERT: A 305 CYS cc_start: 0.8404 (m) cc_final: 0.7879 (t) REVERT: B 129 ARG cc_start: 0.8353 (mtp180) cc_final: 0.8046 (tpt90) REVERT: B 134 ARG cc_start: 0.8668 (ptt-90) cc_final: 0.8426 (ptt-90) REVERT: B 217 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.7780 (pmt) REVERT: C 21 MET cc_start: 0.7893 (mmm) cc_final: 0.6698 (tmm) REVERT: E 183 GLN cc_start: 0.8407 (mt0) cc_final: 0.8194 (mt0) REVERT: E 186 GLN cc_start: 0.8495 (tp40) cc_final: 0.8120 (tm-30) REVERT: R 165 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7982 (ttt) REVERT: R 235 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7874 (tp) REVERT: R 239 LEU cc_start: 0.7216 (mt) cc_final: 0.6748 (tp) REVERT: R 252 ARG cc_start: 0.6790 (OUTLIER) cc_final: 0.5743 (mpp80) REVERT: R 283 PHE cc_start: 0.7993 (t80) cc_final: 0.6328 (m-10) REVERT: R 303 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.7034 (mmm160) REVERT: R 318 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7513 (mm) outliers start: 36 outliers final: 22 residues processed: 158 average time/residue: 0.7346 time to fit residues: 122.3783 Evaluate side-chains 165 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 192 ASP Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 303 ARG Chi-restraints excluded: chain R residue 304 MET Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 386 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 89 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 48 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 0.0370 chunk 47 optimal weight: 0.6980 chunk 81 optimal weight: 0.0570 chunk 110 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.174635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.139205 restraints weight = 9207.032| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.59 r_work: 0.3348 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9155 Z= 0.103 Angle : 0.465 6.274 12428 Z= 0.249 Chirality : 0.041 0.143 1425 Planarity : 0.003 0.055 1571 Dihedral : 4.239 52.260 1254 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.69 % Allowed : 13.34 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 1.49 (0.25), residues: 1144 helix: 2.75 (0.26), residues: 391 sheet: 0.28 (0.29), residues: 303 loop : -0.02 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 150 TYR 0.014 0.001 TYR R 341 PHE 0.014 0.001 PHE B 151 TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 9151) covalent geometry : angle 0.46471 (12420) SS BOND : bond 0.00200 ( 4) SS BOND : angle 0.50195 ( 8) hydrogen bonds : bond 0.03644 ( 467) hydrogen bonds : angle 4.43535 ( 1311) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.370 Fit side-chains REVERT: A 24 ARG cc_start: 0.7895 (ttm110) cc_final: 0.7569 (mtm-85) REVERT: A 25 GLU cc_start: 0.7736 (tt0) cc_final: 0.7520 (mt-10) REVERT: A 208 ARG cc_start: 0.7907 (ttm-80) cc_final: 0.7337 (ttm110) REVERT: A 305 CYS cc_start: 0.8246 (m) cc_final: 0.7708 (t) REVERT: B 124 TYR cc_start: 0.8973 (m-80) cc_final: 0.8725 (m-80) REVERT: B 129 ARG cc_start: 0.8296 (mtp180) cc_final: 0.7987 (tpt90) REVERT: B 134 ARG cc_start: 0.8591 (ptt-90) cc_final: 0.8388 (ptt-90) REVERT: B 217 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.7765 (pmt) REVERT: C 21 MET cc_start: 0.7835 (mmm) cc_final: 0.6622 (tmm) REVERT: E 43 LYS cc_start: 0.8115 (mmtm) cc_final: 0.7477 (mtmt) REVERT: E 183 GLN cc_start: 0.8360 (mt0) cc_final: 0.8135 (mt0) REVERT: R 235 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7829 (tp) REVERT: R 239 LEU cc_start: 0.7137 (mt) cc_final: 0.6679 (tp) REVERT: R 252 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.5648 (mpp80) REVERT: R 283 PHE cc_start: 0.7979 (t80) cc_final: 0.6320 (m-10) outliers start: 26 outliers final: 17 residues processed: 161 average time/residue: 0.7448 time to fit residues: 126.6461 Evaluate side-chains 159 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 192 ASP Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 304 MET Chi-restraints excluded: chain R residue 386 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 88 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 31 optimal weight: 0.0980 chunk 69 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.173650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.138173 restraints weight = 9142.824| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.63 r_work: 0.3334 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9155 Z= 0.123 Angle : 0.491 7.011 12428 Z= 0.263 Chirality : 0.041 0.143 1425 Planarity : 0.003 0.055 1571 Dihedral : 4.312 52.312 1254 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.59 % Allowed : 13.34 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 1.44 (0.25), residues: 1144 helix: 2.69 (0.26), residues: 391 sheet: 0.21 (0.28), residues: 306 loop : 0.01 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 304 TYR 0.013 0.001 TYR R 342 PHE 0.016 0.001 PHE B 151 TRP 0.015 0.002 TRP R 248 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9151) covalent geometry : angle 0.49125 (12420) SS BOND : bond 0.00179 ( 4) SS BOND : angle 0.57358 ( 8) hydrogen bonds : bond 0.03837 ( 467) hydrogen bonds : angle 4.51983 ( 1311) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.313 Fit side-chains REVERT: A 24 ARG cc_start: 0.7845 (ttm110) cc_final: 0.7367 (mtm110) REVERT: A 25 GLU cc_start: 0.7708 (tt0) cc_final: 0.7508 (mt-10) REVERT: A 207 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7374 (tt0) REVERT: A 208 ARG cc_start: 0.7907 (ttm-80) cc_final: 0.7331 (ttm110) REVERT: A 209 LYS cc_start: 0.8100 (pttp) cc_final: 0.7772 (ptmt) REVERT: A 305 CYS cc_start: 0.8255 (m) cc_final: 0.7692 (t) REVERT: B 129 ARG cc_start: 0.8287 (mtp180) cc_final: 0.7972 (tpt90) REVERT: B 134 ARG cc_start: 0.8586 (ptt-90) cc_final: 0.8334 (ptt-90) REVERT: B 217 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.7700 (pmt) REVERT: C 21 MET cc_start: 0.7808 (mmm) cc_final: 0.6618 (tmm) REVERT: E 43 LYS cc_start: 0.8121 (mmtm) cc_final: 0.7487 (mtmt) REVERT: E 183 GLN cc_start: 0.8312 (mt0) cc_final: 0.8097 (mt0) REVERT: E 186 GLN cc_start: 0.8382 (tp40) cc_final: 0.8035 (tm-30) REVERT: R 235 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7840 (tp) REVERT: R 239 LEU cc_start: 0.7162 (mt) cc_final: 0.6699 (tp) REVERT: R 252 ARG cc_start: 0.6623 (OUTLIER) cc_final: 0.5575 (mpp80) REVERT: R 283 PHE cc_start: 0.7968 (t80) cc_final: 0.6305 (m-10) REVERT: R 303 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6876 (mmm160) REVERT: R 325 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6385 (ptp90) outliers start: 25 outliers final: 18 residues processed: 151 average time/residue: 0.6451 time to fit residues: 102.8162 Evaluate side-chains 160 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 192 ASP Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 303 ARG Chi-restraints excluded: chain R residue 304 MET Chi-restraints excluded: chain R residue 325 ARG Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain L residue 8 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.172622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.136841 restraints weight = 9120.636| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.58 r_work: 0.3317 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9155 Z= 0.144 Angle : 0.514 7.513 12428 Z= 0.274 Chirality : 0.042 0.145 1425 Planarity : 0.004 0.055 1571 Dihedral : 4.429 52.290 1254 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.00 % Allowed : 13.13 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 1.39 (0.25), residues: 1144 helix: 2.64 (0.26), residues: 392 sheet: 0.20 (0.28), residues: 306 loop : -0.03 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 304 TYR 0.014 0.002 TYR E 103 PHE 0.018 0.001 PHE B 151 TRP 0.015 0.002 TRP R 248 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9151) covalent geometry : angle 0.51356 (12420) SS BOND : bond 0.00206 ( 4) SS BOND : angle 0.56702 ( 8) hydrogen bonds : bond 0.04037 ( 467) hydrogen bonds : angle 4.60606 ( 1311) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3709.06 seconds wall clock time: 63 minutes 56.03 seconds (3836.03 seconds total)