Starting phenix.real_space_refine on Thu Mar 13 13:54:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wwn_37894/03_2025/8wwn_37894.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wwn_37894/03_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_37894/03_2025/8wwn_37894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wwn_37894/03_2025/8wwn_37894.map" model { file = "/net/cci-nas-00/data/ceres_data/8wwn_37894/03_2025/8wwn_37894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wwn_37894/03_2025/8wwn_37894.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.084 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3} 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: 5.22, per 1000 atoms: 0.58 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: 2.05 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.98 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: 2.46 Time building geometry restraints manager: 2.45 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: 0.900 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.520 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.220 ------------------------------------------------------------------------------- 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 9151 Z= 0.148 Angle : 0.442 5.461 12420 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.25), 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 TRP 0.010 0.001 TRP B 339 HIS 0.003 0.001 HIS E 35 PHE 0.016 0.001 PHE B 151 TYR 0.009 0.001 TYR E 103 ARG 0.003 0.000 ARG E 38 *********************** 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 : 1.023 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: 0.7236 (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: 1.5236 time to fit residues: 303.9662 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 : 1.077 ------------------------------------------------------------------------------- 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 95 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 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 = 0.3942 r_free = 0.3942 target = 0.172774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.137264 restraints weight = 9055.384| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.61 r_work: 0.3308 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9151 Z= 0.223 Angle : 0.537 6.114 12420 Z= 0.293 Chirality : 0.043 0.150 1425 Planarity : 0.004 0.054 1571 Dihedral : 4.893 55.407 1257 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.00 % Allowed : 9.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.25), residues: 1144 helix: 2.05 (0.26), residues: 397 sheet: 0.68 (0.29), residues: 301 loop : 0.25 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS A 188 PHE 0.017 0.002 PHE B 151 TYR 0.013 0.001 TYR R 341 ARG 0.003 0.000 ARG B 251 *********************** 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 184 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8337 (ttm170) cc_final: 0.8112 (ttp-110) REVERT: A 22 ASN cc_start: 0.8354 (m-40) cc_final: 0.8050 (m-40) REVERT: A 24 ARG cc_start: 0.8000 (ttm110) cc_final: 0.7406 (mtt90) REVERT: A 25 GLU cc_start: 0.7850 (tt0) cc_final: 0.7621 (mt-10) REVERT: A 46 LYS cc_start: 0.7548 (ttpm) cc_final: 0.7045 (ttpt) REVERT: A 208 ARG cc_start: 0.8071 (ttm-80) cc_final: 0.7498 (ttm110) REVERT: A 305 CYS cc_start: 0.8409 (m) cc_final: 0.7947 (t) REVERT: A 312 LYS cc_start: 0.8377 (tppt) cc_final: 0.8109 (mptt) REVERT: B 124 TYR cc_start: 0.8975 (m-80) cc_final: 0.8726 (m-80) REVERT: B 197 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7533 (mtt-85) REVERT: C 21 MET cc_start: 0.7741 (mmm) cc_final: 0.6717 (tmm) REVERT: R 165 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7628 (ttt) REVERT: R 235 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7781 (tt) REVERT: R 239 LEU cc_start: 0.7228 (mt) cc_final: 0.6783 (tp) REVERT: R 266 ARG cc_start: 0.7641 (mtp180) cc_final: 0.7096 (mtm110) REVERT: R 359 VAL cc_start: 0.8037 (t) cc_final: 0.7807 (m) outliers start: 29 outliers final: 10 residues processed: 163 average time/residue: 1.4042 time to fit residues: 242.1231 Evaluate side-chains 157 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 L residue 8 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 99 optimal weight: 0.1980 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 0.0870 chunk 74 optimal weight: 10.0000 chunk 10 optimal weight: 0.0980 chunk 95 optimal weight: 0.0570 chunk 101 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 overall best weight: 0.2676 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.176283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.141380 restraints weight = 9254.706| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.58 r_work: 0.3377 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9151 Z= 0.132 Angle : 0.457 5.060 12420 Z= 0.248 Chirality : 0.041 0.147 1425 Planarity : 0.003 0.051 1571 Dihedral : 4.173 50.182 1255 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.90 % Allowed : 10.86 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.25), residues: 1144 helix: 2.57 (0.26), residues: 393 sheet: 0.59 (0.30), residues: 287 loop : 0.24 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.012 0.001 PHE B 151 TYR 0.015 0.001 TYR E 190 ARG 0.002 0.000 ARG A 21 *********************** 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 190 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.962 Fit side-chains REVERT: A 24 ARG cc_start: 0.7854 (ttm110) cc_final: 0.7331 (mtm110) REVERT: A 208 ARG cc_start: 0.7954 (ttm-80) cc_final: 0.7384 (ttm110) REVERT: A 209 LYS cc_start: 0.8150 (pttp) cc_final: 0.7793 (ptmm) REVERT: A 304 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.8002 (tm-30) REVERT: A 305 CYS cc_start: 0.8265 (m) cc_final: 0.7850 (t) REVERT: B 124 TYR cc_start: 0.8919 (m-80) cc_final: 0.8704 (m-80) REVERT: B 129 ARG cc_start: 0.8194 (mtp180) cc_final: 0.7956 (tpt90) REVERT: B 217 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.7520 (pmt) REVERT: C 21 MET cc_start: 0.7789 (mmm) cc_final: 0.6779 (tmm) REVERT: E 46 GLU cc_start: 0.8560 (tt0) cc_final: 0.8328 (tt0) REVERT: R 165 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7730 (ttt) REVERT: R 235 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7759 (tt) REVERT: R 239 LEU cc_start: 0.7164 (mt) cc_final: 0.6723 (tp) REVERT: R 252 ARG cc_start: 0.6614 (OUTLIER) cc_final: 0.5824 (mpp80) REVERT: R 266 ARG cc_start: 0.7643 (mtp180) cc_final: 0.6939 (mtm110) outliers start: 28 outliers final: 5 residues processed: 172 average time/residue: 1.3936 time to fit residues: 253.3695 Evaluate side-chains 153 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 304 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 235 LEU Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR 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 102 optimal weight: 2.9990 chunk 15 optimal weight: 0.0670 chunk 106 optimal weight: 0.6980 chunk 97 optimal weight: 0.1980 chunk 96 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 98 optimal weight: 0.0980 chunk 43 optimal weight: 1.9990 chunk 79 optimal weight: 0.0270 chunk 6 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 overall best weight: 0.2176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.177431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.143079 restraints weight = 9155.848| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.64 r_work: 0.3397 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9151 Z= 0.120 Angle : 0.441 5.060 12420 Z= 0.239 Chirality : 0.040 0.150 1425 Planarity : 0.003 0.048 1571 Dihedral : 3.987 50.704 1254 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.79 % Allowed : 11.69 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.25), residues: 1144 helix: 2.80 (0.26), residues: 388 sheet: 0.47 (0.29), residues: 291 loop : 0.25 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS A 188 PHE 0.011 0.001 PHE B 151 TYR 0.013 0.001 TYR E 190 ARG 0.001 0.000 ARG E 72 *********************** 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 177 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7827 (ttm110) cc_final: 0.7293 (mtm110) REVERT: A 208 ARG cc_start: 0.7901 (ttm-80) cc_final: 0.7360 (ttm110) REVERT: A 209 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7811 (ptmm) REVERT: A 305 CYS cc_start: 0.8239 (m) cc_final: 0.7791 (t) REVERT: B 124 TYR cc_start: 0.8956 (m-80) cc_final: 0.8709 (m-80) REVERT: B 129 ARG cc_start: 0.8196 (mtp180) cc_final: 0.7960 (tpt90) REVERT: B 217 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.7469 (pmt) REVERT: C 21 MET cc_start: 0.7801 (mmm) cc_final: 0.6771 (tmm) REVERT: E 46 GLU cc_start: 0.8595 (tt0) cc_final: 0.8389 (tt0) REVERT: R 165 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7843 (ttt) REVERT: R 235 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7815 (tt) REVERT: R 239 LEU cc_start: 0.7128 (mt) cc_final: 0.6660 (tp) REVERT: R 252 ARG cc_start: 0.6610 (OUTLIER) cc_final: 0.5799 (mpp80) REVERT: R 266 ARG cc_start: 0.7735 (mtp180) cc_final: 0.7029 (mtm110) REVERT: R 283 PHE cc_start: 0.8033 (t80) cc_final: 0.6351 (m-10) outliers start: 27 outliers final: 11 residues processed: 159 average time/residue: 1.5532 time to fit residues: 260.5817 Evaluate side-chains 158 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET 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 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 386 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 73 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 80 optimal weight: 0.0050 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.174675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.139283 restraints weight = 9162.444| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.61 r_work: 0.3340 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9151 Z= 0.178 Angle : 0.476 5.135 12420 Z= 0.257 Chirality : 0.041 0.144 1425 Planarity : 0.003 0.049 1571 Dihedral : 4.183 51.482 1254 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.90 % Allowed : 11.79 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.25), residues: 1144 helix: 2.78 (0.26), residues: 391 sheet: 0.43 (0.29), residues: 302 loop : 0.11 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 248 HIS 0.005 0.001 HIS E 35 PHE 0.014 0.001 PHE B 151 TYR 0.013 0.001 TYR R 342 ARG 0.002 0.000 ARG B 251 *********************** 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 174 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.925 Fit side-chains REVERT: A 24 ARG cc_start: 0.7824 (ttm110) cc_final: 0.7316 (mtm110) REVERT: A 208 ARG cc_start: 0.7921 (ttm-80) cc_final: 0.7324 (ttm110) REVERT: A 209 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7848 (ptmm) REVERT: A 304 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7970 (tm-30) REVERT: A 305 CYS cc_start: 0.8278 (m) cc_final: 0.7838 (t) REVERT: B 124 TYR cc_start: 0.9002 (m-80) cc_final: 0.8734 (m-80) REVERT: B 129 ARG cc_start: 0.8203 (mtp180) cc_final: 0.7971 (tpt90) REVERT: B 217 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.7467 (pmt) REVERT: C 21 MET cc_start: 0.7867 (mmm) cc_final: 0.6803 (tmm) REVERT: E 186 GLN cc_start: 0.8435 (tp40) cc_final: 0.8100 (tt0) REVERT: R 165 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7899 (ttt) REVERT: R 235 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7836 (tp) REVERT: R 239 LEU cc_start: 0.7129 (mt) cc_final: 0.6647 (tp) REVERT: R 252 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.5557 (mpp80) REVERT: R 283 PHE cc_start: 0.8003 (t80) cc_final: 0.6252 (m-10) outliers start: 28 outliers final: 13 residues processed: 160 average time/residue: 1.3768 time to fit residues: 233.2044 Evaluate side-chains 164 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 304 GLN 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 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 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: 0.0670 chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 84 optimal weight: 0.0980 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN ** B 340 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 = 0.3972 r_free = 0.3972 target = 0.175331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.139586 restraints weight = 9066.811| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.59 r_work: 0.3324 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9151 Z= 0.159 Angle : 0.467 7.449 12420 Z= 0.251 Chirality : 0.041 0.144 1425 Planarity : 0.003 0.050 1571 Dihedral : 4.163 51.840 1254 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.10 % Allowed : 12.20 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.25), residues: 1144 helix: 2.76 (0.26), residues: 391 sheet: 0.39 (0.29), residues: 302 loop : 0.12 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.001 PHE B 151 TYR 0.013 0.001 TYR R 342 ARG 0.002 0.000 ARG B 251 *********************** 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 178 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 1.787 Fit side-chains REVERT: A 24 ARG cc_start: 0.7920 (ttm110) cc_final: 0.7602 (mtm-85) REVERT: A 208 ARG cc_start: 0.7956 (ttm-80) cc_final: 0.7365 (ttm110) REVERT: A 209 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7940 (ptmm) REVERT: A 304 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7420 (tt0) REVERT: A 305 CYS cc_start: 0.8187 (m) cc_final: 0.7654 (t) REVERT: B 129 ARG cc_start: 0.8257 (mtp180) cc_final: 0.8026 (tpt90) REVERT: B 217 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.7530 (pmt) REVERT: C 21 MET cc_start: 0.7890 (mmm) cc_final: 0.6726 (tmm) REVERT: E 186 GLN cc_start: 0.8453 (tp40) cc_final: 0.8123 (tt0) REVERT: R 165 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7979 (ttt) REVERT: R 235 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7879 (tt) REVERT: R 239 LEU cc_start: 0.7155 (mt) cc_final: 0.6681 (tp) REVERT: R 252 ARG cc_start: 0.6700 (OUTLIER) cc_final: 0.5628 (mpp80) REVERT: R 283 PHE cc_start: 0.8033 (t80) cc_final: 0.6318 (m-10) outliers start: 30 outliers final: 14 residues processed: 158 average time/residue: 1.4912 time to fit residues: 251.9408 Evaluate side-chains 160 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 304 GLN 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 B residue 270 ILE 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 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 386 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.174826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.139327 restraints weight = 9190.932| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.62 r_work: 0.3342 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9151 Z= 0.175 Angle : 0.473 5.201 12420 Z= 0.254 Chirality : 0.041 0.144 1425 Planarity : 0.003 0.051 1571 Dihedral : 4.198 52.003 1254 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.90 % Allowed : 12.72 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.25), residues: 1144 helix: 2.78 (0.26), residues: 391 sheet: 0.36 (0.29), residues: 302 loop : 0.09 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.001 PHE B 151 TYR 0.013 0.001 TYR R 342 ARG 0.002 0.000 ARG B 251 *********************** 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 169 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.938 Fit side-chains REVERT: A 24 ARG cc_start: 0.7861 (ttm110) cc_final: 0.7383 (mtm110) REVERT: A 208 ARG cc_start: 0.7956 (ttm-80) cc_final: 0.7392 (ttm110) REVERT: A 304 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7480 (tt0) REVERT: A 305 CYS cc_start: 0.8225 (m) cc_final: 0.7736 (t) REVERT: B 129 ARG cc_start: 0.8224 (mtp180) cc_final: 0.7997 (tpt90) REVERT: B 217 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.7460 (pmt) REVERT: C 21 MET cc_start: 0.7871 (mmm) cc_final: 0.6705 (tmm) REVERT: E 186 GLN cc_start: 0.8405 (tp40) cc_final: 0.8088 (tt0) REVERT: R 165 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.8018 (ttt) REVERT: R 235 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7833 (tp) REVERT: R 239 LEU cc_start: 0.7142 (mt) cc_final: 0.6670 (tp) REVERT: R 252 ARG cc_start: 0.6701 (OUTLIER) cc_final: 0.5590 (mpp80) REVERT: R 283 PHE cc_start: 0.8001 (t80) cc_final: 0.6313 (m-10) outliers start: 28 outliers final: 16 residues processed: 151 average time/residue: 1.6002 time to fit residues: 255.2721 Evaluate side-chains 160 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 GLN 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 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 386 THR Chi-restraints excluded: chain L residue 8 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 22 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.173741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.138874 restraints weight = 9257.598| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.70 r_work: 0.3319 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9151 Z= 0.216 Angle : 0.496 5.723 12420 Z= 0.267 Chirality : 0.042 0.145 1425 Planarity : 0.004 0.052 1571 Dihedral : 4.311 52.110 1254 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.52 % Allowed : 11.89 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.25), residues: 1144 helix: 2.73 (0.26), residues: 391 sheet: 0.31 (0.29), residues: 304 loop : 0.04 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 248 HIS 0.005 0.001 HIS E 35 PHE 0.016 0.001 PHE B 151 TYR 0.013 0.001 TYR R 342 ARG 0.002 0.000 ARG B 251 *********************** 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 173 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 0.956 Fit side-chains REVERT: A 24 ARG cc_start: 0.7879 (ttm110) cc_final: 0.7604 (mtm-85) REVERT: A 208 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7379 (ttm110) REVERT: A 209 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8041 (ptmm) REVERT: A 304 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7829 (tm-30) REVERT: A 305 CYS cc_start: 0.8314 (m) cc_final: 0.7903 (t) REVERT: B 129 ARG cc_start: 0.8240 (mtp180) cc_final: 0.8009 (tpt90) REVERT: B 217 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.7498 (pmt) REVERT: C 21 MET cc_start: 0.7842 (mmm) cc_final: 0.6677 (tmm) REVERT: E 186 GLN cc_start: 0.8463 (tp40) cc_final: 0.8110 (tm-30) REVERT: R 165 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.8038 (ttt) REVERT: R 235 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7867 (tp) REVERT: R 239 LEU cc_start: 0.7151 (mt) cc_final: 0.6675 (tp) REVERT: R 252 ARG cc_start: 0.6754 (OUTLIER) cc_final: 0.5683 (mpp80) REVERT: R 283 PHE cc_start: 0.8014 (t80) cc_final: 0.6314 (m-10) outliers start: 34 outliers final: 21 residues processed: 153 average time/residue: 1.3863 time to fit residues: 224.5429 Evaluate side-chains 166 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain B residue 61 MET 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 7 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN ** B 340 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 = 0.3954 r_free = 0.3954 target = 0.173649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.138029 restraints weight = 9200.750| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.63 r_work: 0.3332 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9151 Z= 0.204 Angle : 0.501 8.821 12420 Z= 0.266 Chirality : 0.042 0.145 1425 Planarity : 0.003 0.052 1571 Dihedral : 4.329 52.172 1254 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.00 % Allowed : 13.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.25), residues: 1144 helix: 2.72 (0.26), residues: 391 sheet: 0.29 (0.28), residues: 304 loop : 0.02 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 248 HIS 0.005 0.001 HIS E 35 PHE 0.015 0.001 PHE B 151 TYR 0.013 0.001 TYR E 103 ARG 0.002 0.000 ARG B 251 *********************** 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 170 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 1.086 Fit side-chains REVERT: A 24 ARG cc_start: 0.7863 (ttm110) cc_final: 0.7592 (mtm-85) REVERT: A 208 ARG cc_start: 0.7970 (ttm-80) cc_final: 0.7383 (ttm110) REVERT: A 209 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7992 (ptmm) REVERT: A 304 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7912 (tm-30) REVERT: A 305 CYS cc_start: 0.8294 (m) cc_final: 0.7945 (t) REVERT: B 129 ARG cc_start: 0.8231 (mtp180) cc_final: 0.8004 (tpt90) REVERT: B 217 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.7476 (pmt) REVERT: C 21 MET cc_start: 0.7841 (mmm) cc_final: 0.6663 (tmm) REVERT: E 186 GLN cc_start: 0.8422 (tp40) cc_final: 0.8058 (tm-30) REVERT: R 165 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.8028 (ttt) REVERT: R 235 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7862 (tp) REVERT: R 239 LEU cc_start: 0.7165 (mt) cc_final: 0.6698 (tp) REVERT: R 252 ARG cc_start: 0.6754 (OUTLIER) cc_final: 0.5679 (mpp80) REVERT: R 283 PHE cc_start: 0.8002 (t80) cc_final: 0.6310 (m-10) outliers start: 29 outliers final: 21 residues processed: 155 average time/residue: 1.4163 time to fit residues: 232.5012 Evaluate side-chains 164 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain B residue 61 MET 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 109 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 95 optimal weight: 0.0770 chunk 4 optimal weight: 7.9990 chunk 104 optimal weight: 0.3980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN ** B 340 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 = 0.3967 r_free = 0.3967 target = 0.174912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.139528 restraints weight = 9196.165| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.61 r_work: 0.3355 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9151 Z= 0.156 Angle : 0.477 8.382 12420 Z= 0.254 Chirality : 0.041 0.144 1425 Planarity : 0.003 0.052 1571 Dihedral : 4.230 52.237 1254 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.25), residues: 1144 helix: 2.77 (0.26), residues: 393 sheet: 0.27 (0.28), residues: 304 loop : 0.02 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.001 PHE B 151 TYR 0.012 0.001 TYR R 341 ARG 0.002 0.000 ARG B 251 ********************** 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 : 1.012 Fit side-chains REVERT: A 24 ARG cc_start: 0.7818 (ttm110) cc_final: 0.7349 (mtm110) REVERT: A 208 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7312 (ttm110) REVERT: A 304 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7743 (tm-30) REVERT: A 305 CYS cc_start: 0.8283 (m) cc_final: 0.7924 (t) REVERT: B 129 ARG cc_start: 0.8192 (mtp180) cc_final: 0.7969 (tpt90) REVERT: B 217 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.7394 (pmt) REVERT: C 21 MET cc_start: 0.7819 (mmm) cc_final: 0.6663 (tmm) REVERT: E 186 GLN cc_start: 0.8364 (tp40) cc_final: 0.8017 (tm-30) REVERT: R 165 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7981 (ttt) REVERT: R 235 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7828 (tp) REVERT: R 239 LEU cc_start: 0.7122 (mt) cc_final: 0.6657 (tp) REVERT: R 252 ARG cc_start: 0.6591 (OUTLIER) cc_final: 0.5574 (mpp80) REVERT: R 283 PHE cc_start: 0.7973 (t80) cc_final: 0.6268 (m-10) outliers start: 25 outliers final: 16 residues processed: 151 average time/residue: 1.9120 time to fit residues: 306.8321 Evaluate side-chains 160 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 GLN 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 386 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 69 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 0.0020 chunk 13 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.173877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.138078 restraints weight = 9204.398| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.64 r_work: 0.3335 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9151 Z= 0.204 Angle : 0.501 8.660 12420 Z= 0.266 Chirality : 0.042 0.144 1425 Planarity : 0.003 0.052 1571 Dihedral : 4.324 52.236 1254 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.25), residues: 1144 helix: 2.73 (0.26), residues: 393 sheet: 0.25 (0.28), residues: 304 loop : -0.03 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 248 HIS 0.005 0.001 HIS E 35 PHE 0.015 0.001 PHE B 151 TYR 0.013 0.001 TYR R 342 ARG 0.002 0.000 ARG B 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8460.94 seconds wall clock time: 147 minutes 12.26 seconds (8832.26 seconds total)