Starting phenix.real_space_refine on Wed Mar 12 15:59:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zsj_60417/03_2025/8zsj_60417.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zsj_60417/03_2025/8zsj_60417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zsj_60417/03_2025/8zsj_60417.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zsj_60417/03_2025/8zsj_60417.map" model { file = "/net/cci-nas-00/data/ceres_data/8zsj_60417/03_2025/8zsj_60417.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zsj_60417/03_2025/8zsj_60417.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 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 60 5.16 5 C 5166 2.51 5 N 1390 2.21 5 O 1502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8118 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1889 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2594 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 2200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2200 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 11, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 32 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1, 'water': 4} Link IDs: {None: 4} Time building chain proxies: 5.58, per 1000 atoms: 0.69 Number of scatterers: 8118 At special positions: 0 Unit cell: (80.704, 99.008, 133.952, 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 60 16.00 O 1502 8.00 N 1390 7.00 C 5166 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " 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: 2.24 Conformation dependent library (CDL) restraints added in 1.0 seconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 43.0% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.557A pdb=" N GLU A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 95 through 101 removed outlier: 3.680A pdb=" N ASN A 101 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.245A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 183 through 204 removed outlier: 3.756A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.658A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 23 through 52 removed outlier: 3.667A pdb=" N SER R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU R 29 " --> pdb=" O SER R 25 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LYS R 52 " --> pdb=" O ILE R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 86 Proline residue: R 78 - end of helix Processing helix chain 'R' and resid 92 through 127 Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 136 through 161 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 169 through 179 removed outlier: 3.777A pdb=" N TYR R 173 " --> pdb=" O GLU R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 199 Processing helix chain 'R' and resid 199 through 230 removed outlier: 3.549A pdb=" N ILE R 205 " --> pdb=" O ILE R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 247 through 274 removed outlier: 3.631A pdb=" N LYS R 251 " --> pdb=" O ARG R 247 " (cutoff:3.500A) Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 282 through 305 removed outlier: 3.522A pdb=" N ASN R 286 " --> pdb=" O PRO R 282 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP R 291 " --> pdb=" O ASP R 287 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER R 297 " --> pdb=" O GLY R 293 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 318 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 75 removed outlier: 6.446A pdb=" N HIS A 41 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N PHE A 84 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 43 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL A 86 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LEU A 45 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 9.644A pdb=" N ALA A 105 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG A 42 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ILE A 107 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU A 44 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL A 109 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU A 46 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N ASP A 111 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.520A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.820A 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: 3.513A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.873A 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: 6.416A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.604A 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: 6.514A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.184A 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: 6.697A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.149A 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: 6.578A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.773A 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: 6.401A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.976A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1218 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: 2.36 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1314 1.31 - 1.43: 2289 1.43 - 1.56: 4604 1.56 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 8294 Sorted by residual: bond pdb=" C CYS B 294 " pdb=" O CYS B 294 " ideal model delta sigma weight residual 1.235 1.179 0.056 1.28e-02 6.10e+03 1.94e+01 bond pdb=" CA LEU B 308 " pdb=" C LEU B 308 " ideal model delta sigma weight residual 1.528 1.485 0.043 1.04e-02 9.25e+03 1.72e+01 bond pdb=" C LEU B 210 " pdb=" O LEU B 210 " ideal model delta sigma weight residual 1.236 1.188 0.048 1.22e-02 6.72e+03 1.52e+01 bond pdb=" CA LEU B 210 " pdb=" C LEU B 210 " ideal model delta sigma weight residual 1.524 1.480 0.044 1.23e-02 6.61e+03 1.29e+01 bond pdb=" CA GLU A 92 " pdb=" CB GLU A 92 " ideal model delta sigma weight residual 1.528 1.482 0.046 1.35e-02 5.49e+03 1.16e+01 ... (remaining 8289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 10983 2.08 - 4.17: 242 4.17 - 6.25: 21 6.25 - 8.34: 2 8.34 - 10.42: 3 Bond angle restraints: 11251 Sorted by residual: angle pdb=" N PHE A 70 " pdb=" CA PHE A 70 " pdb=" C PHE A 70 " ideal model delta sigma weight residual 110.30 100.05 10.25 1.50e+00 4.44e-01 4.67e+01 angle pdb=" C PHE A 70 " pdb=" CA PHE A 70 " pdb=" CB PHE A 70 " ideal model delta sigma weight residual 110.06 118.15 -8.09 1.39e+00 5.18e-01 3.39e+01 angle pdb=" N VAL A 57 " pdb=" CA VAL A 57 " pdb=" C VAL A 57 " ideal model delta sigma weight residual 112.17 107.42 4.75 9.50e-01 1.11e+00 2.50e+01 angle pdb=" N GLU R 170 " pdb=" CA GLU R 170 " pdb=" C GLU R 170 " ideal model delta sigma weight residual 111.71 106.56 5.15 1.15e+00 7.56e-01 2.01e+01 angle pdb=" N GLY R 167 " pdb=" CA GLY R 167 " pdb=" C GLY R 167 " ideal model delta sigma weight residual 115.64 109.53 6.11 1.46e+00 4.69e-01 1.75e+01 ... (remaining 11246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 4484 16.07 - 32.13: 371 32.13 - 48.20: 85 48.20 - 64.27: 15 64.27 - 80.34: 8 Dihedral angle restraints: 4963 sinusoidal: 1949 harmonic: 3014 Sorted by residual: dihedral pdb=" CA HIS R 50 " pdb=" C HIS R 50 " pdb=" N PHE R 51 " pdb=" CA PHE R 51 " ideal model delta harmonic sigma weight residual -180.00 -155.62 -24.38 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 53.06 39.94 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CG ARG N 67 " pdb=" CD ARG N 67 " pdb=" NE ARG N 67 " pdb=" CZ ARG N 67 " ideal model delta sinusoidal sigma weight residual 90.00 131.74 -41.74 2 1.50e+01 4.44e-03 9.45e+00 ... (remaining 4960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1063 0.067 - 0.133: 178 0.133 - 0.200: 21 0.200 - 0.266: 3 0.266 - 0.333: 1 Chirality restraints: 1266 Sorted by residual: chirality pdb=" CA THR N 91 " pdb=" N THR N 91 " pdb=" C THR N 91 " pdb=" CB THR N 91 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA ASP R 287 " pdb=" N ASP R 287 " pdb=" C ASP R 287 " pdb=" CB ASP R 287 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA VAL A 57 " pdb=" N VAL A 57 " pdb=" C VAL A 57 " pdb=" CB VAL A 57 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1263 not shown) Planarity restraints: 1429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 83 " 0.418 9.50e-02 1.11e+02 1.88e-01 2.15e+01 pdb=" NE ARG R 83 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG R 83 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG R 83 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG R 83 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR R 308 " 0.071 5.00e-02 4.00e+02 1.07e-01 1.83e+01 pdb=" N PRO R 309 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO R 309 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO R 309 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 312 " 0.383 9.50e-02 1.11e+02 1.72e-01 1.80e+01 pdb=" NE ARG R 312 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG R 312 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG R 312 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG R 312 " 0.013 2.00e-02 2.50e+03 ... (remaining 1426 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1105 2.75 - 3.29: 7970 3.29 - 3.83: 14027 3.83 - 4.36: 17110 4.36 - 4.90: 29488 Nonbonded interactions: 69700 Sorted by model distance: nonbonded pdb=" OG SER N 7 " pdb=" OG SER N 21 " model vdw 2.216 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.231 3.040 nonbonded pdb=" OG1 THR R 56 " pdb=" OD1 ASN R 59 " model vdw 2.253 3.040 nonbonded pdb=" OG SER B 227 " pdb=" O PRO N 100 " model vdw 2.272 3.040 nonbonded pdb=" OD2 ASP R 103 " pdb=" O HOH R 501 " model vdw 2.273 3.040 ... (remaining 69695 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: 2.090 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.120 Find NCS groups from input model: 0.070 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:14.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 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 : 0.005 0.056 8294 Z= 0.324 Angle : 0.684 10.422 11251 Z= 0.444 Chirality : 0.051 0.333 1266 Planarity : 0.011 0.188 1429 Dihedral : 12.911 80.336 3006 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.12 % Allowed : 1.16 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.27), residues: 1021 helix: 2.24 (0.25), residues: 387 sheet: -0.06 (0.35), residues: 215 loop : -0.62 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 291 HIS 0.004 0.001 HIS R 63 PHE 0.018 0.001 PHE R 91 TYR 0.010 0.001 TYR R 308 ARG 0.016 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.7879 (m-30) cc_final: 0.7586 (m-30) REVERT: N 53 GLN cc_start: 0.8750 (mp10) cc_final: 0.8533 (mp10) REVERT: R 95 PHE cc_start: 0.7456 (t80) cc_final: 0.7231 (t80) REVERT: R 302 MET cc_start: 0.7989 (mtt) cc_final: 0.7758 (mtp) outliers start: 1 outliers final: 1 residues processed: 178 average time/residue: 1.4411 time to fit residues: 270.7402 Evaluate side-chains 142 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 184 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 0.0470 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN B 17 GLN B 44 GLN B 237 ASN B 239 ASN B 259 GLN B 340 ASN N 3 GLN N 39 GLN N 77 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.149973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.115047 restraints weight = 10272.014| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.53 r_work: 0.3273 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8294 Z= 0.227 Angle : 0.546 10.230 11251 Z= 0.291 Chirality : 0.042 0.159 1266 Planarity : 0.005 0.073 1429 Dihedral : 4.318 27.525 1191 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.73 % Allowed : 11.45 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.27), residues: 1021 helix: 2.40 (0.25), residues: 389 sheet: -0.01 (0.35), residues: 212 loop : -0.54 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.005 0.001 HIS R 63 PHE 0.013 0.001 PHE R 51 TYR 0.012 0.001 TYR A 115 ARG 0.007 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.7763 (m-30) cc_final: 0.7371 (m-30) REVERT: A 35 LYS cc_start: 0.8690 (ttpt) cc_final: 0.8384 (ptpt) REVERT: A 151 GLU cc_start: 0.8079 (tp30) cc_final: 0.7858 (tp30) REVERT: B 59 TYR cc_start: 0.8668 (m-80) cc_final: 0.8247 (m-80) REVERT: B 75 GLN cc_start: 0.8157 (tt0) cc_final: 0.7921 (tt0) REVERT: B 134 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6746 (ptm160) REVERT: N 37 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8599 (m) REVERT: N 53 GLN cc_start: 0.8570 (mp10) cc_final: 0.8186 (mp10) REVERT: R 262 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.7941 (mp) REVERT: R 302 MET cc_start: 0.8389 (mtt) cc_final: 0.8010 (mtp) outliers start: 15 outliers final: 4 residues processed: 154 average time/residue: 1.3154 time to fit residues: 214.0077 Evaluate side-chains 147 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 262 ILE Chi-restraints excluded: chain R residue 315 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN B 17 GLN B 44 GLN B 75 GLN B 237 ASN B 259 GLN N 39 GLN N 77 ASN R 296 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.149839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.114743 restraints weight = 10461.560| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.53 r_work: 0.3276 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8294 Z= 0.216 Angle : 0.524 9.971 11251 Z= 0.278 Chirality : 0.041 0.149 1266 Planarity : 0.005 0.061 1429 Dihedral : 4.299 29.904 1191 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.85 % Allowed : 14.80 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.27), residues: 1021 helix: 2.33 (0.25), residues: 396 sheet: -0.11 (0.33), residues: 215 loop : -0.45 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS A 214 PHE 0.014 0.001 PHE R 91 TYR 0.017 0.001 TYR N 60 ARG 0.007 0.000 ARG A 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7155 (pm20) cc_final: 0.6916 (pm20) REVERT: A 15 ASP cc_start: 0.7803 (m-30) cc_final: 0.7383 (m-30) REVERT: A 35 LYS cc_start: 0.8629 (ttpt) cc_final: 0.8353 (mtpt) REVERT: A 151 GLU cc_start: 0.8145 (tp30) cc_final: 0.7781 (tp30) REVERT: B 19 ARG cc_start: 0.7608 (ttp-110) cc_final: 0.7388 (ttp-110) REVERT: B 75 GLN cc_start: 0.8231 (tt0) cc_final: 0.7990 (tt0) REVERT: B 134 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6735 (ptm160) REVERT: B 219 ARG cc_start: 0.8308 (mtt-85) cc_final: 0.7831 (mtp85) REVERT: B 325 MET cc_start: 0.8506 (tpp) cc_final: 0.7988 (mmm) REVERT: N 37 VAL cc_start: 0.8833 (t) cc_final: 0.8581 (m) REVERT: N 53 GLN cc_start: 0.8560 (mp10) cc_final: 0.8213 (mp10) REVERT: R 262 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.7899 (mp) REVERT: R 302 MET cc_start: 0.8355 (mtt) cc_final: 0.7978 (mtp) outliers start: 16 outliers final: 4 residues processed: 159 average time/residue: 1.4901 time to fit residues: 249.8191 Evaluate side-chains 147 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 262 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 1 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 79 optimal weight: 0.0870 chunk 0 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 0.0980 overall best weight: 0.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 44 GLN B 237 ASN B 259 GLN N 31 ASN N 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.151128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.116369 restraints weight = 10356.204| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.51 r_work: 0.3300 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8294 Z= 0.168 Angle : 0.499 9.875 11251 Z= 0.263 Chirality : 0.041 0.145 1266 Planarity : 0.004 0.055 1429 Dihedral : 4.162 28.990 1191 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.66 % Allowed : 15.72 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.27), residues: 1021 helix: 2.39 (0.25), residues: 397 sheet: 0.06 (0.33), residues: 208 loop : -0.47 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS R 63 PHE 0.025 0.001 PHE R 91 TYR 0.020 0.001 TYR N 60 ARG 0.007 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7140 (pm20) cc_final: 0.6880 (pm20) REVERT: A 15 ASP cc_start: 0.7803 (m-30) cc_final: 0.7412 (m-30) REVERT: A 35 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8316 (mtpt) REVERT: A 151 GLU cc_start: 0.8169 (tp30) cc_final: 0.7846 (tp30) REVERT: B 75 GLN cc_start: 0.8296 (tt0) cc_final: 0.8062 (tt0) REVERT: B 134 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6739 (ptm160) REVERT: B 219 ARG cc_start: 0.8297 (mtt-85) cc_final: 0.7803 (mtp85) REVERT: B 325 MET cc_start: 0.8493 (tpp) cc_final: 0.7970 (mmm) REVERT: N 53 GLN cc_start: 0.8527 (mp10) cc_final: 0.8109 (mp10) REVERT: R 262 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.7900 (mp) REVERT: R 302 MET cc_start: 0.8327 (mtt) cc_final: 0.8001 (mtp) outliers start: 23 outliers final: 6 residues processed: 158 average time/residue: 1.1698 time to fit residues: 196.4262 Evaluate side-chains 150 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 226 ASP Chi-restraints excluded: chain R residue 262 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 62 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS B 17 GLN B 44 GLN B 237 ASN B 259 GLN N 77 ASN R 53 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.150323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.115492 restraints weight = 10348.409| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.52 r_work: 0.3289 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8294 Z= 0.194 Angle : 0.501 9.403 11251 Z= 0.265 Chirality : 0.041 0.145 1266 Planarity : 0.004 0.052 1429 Dihedral : 4.046 18.438 1190 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.31 % Allowed : 16.53 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.27), residues: 1021 helix: 2.43 (0.25), residues: 397 sheet: -0.01 (0.32), residues: 215 loop : -0.42 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS R 63 PHE 0.018 0.001 PHE R 91 TYR 0.022 0.001 TYR N 60 ARG 0.007 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7101 (pm20) cc_final: 0.6802 (pm20) REVERT: A 15 ASP cc_start: 0.7800 (m-30) cc_final: 0.7431 (m-30) REVERT: A 34 GLU cc_start: 0.7050 (pp20) cc_final: 0.6848 (pp20) REVERT: A 131 ASN cc_start: 0.9113 (t0) cc_final: 0.8886 (t0) REVERT: A 151 GLU cc_start: 0.8193 (tp30) cc_final: 0.7818 (tp30) REVERT: B 59 TYR cc_start: 0.8647 (m-80) cc_final: 0.8249 (m-80) REVERT: B 75 GLN cc_start: 0.8289 (tt0) cc_final: 0.8086 (tt0) REVERT: B 134 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6730 (ptm160) REVERT: B 155 ASN cc_start: 0.8120 (t0) cc_final: 0.7860 (t0) REVERT: B 219 ARG cc_start: 0.8325 (mtt-85) cc_final: 0.7820 (mtp85) REVERT: B 325 MET cc_start: 0.8500 (tpp) cc_final: 0.7978 (mmm) REVERT: N 53 GLN cc_start: 0.8539 (mp10) cc_final: 0.8141 (mp10) REVERT: R 262 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.7913 (mp) REVERT: R 302 MET cc_start: 0.8344 (mtt) cc_final: 0.7971 (mtp) outliers start: 20 outliers final: 9 residues processed: 156 average time/residue: 1.1390 time to fit residues: 188.7986 Evaluate side-chains 153 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 226 ASP Chi-restraints excluded: chain R residue 262 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 59 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 44 GLN B 237 ASN B 259 GLN N 77 ASN R 53 GLN R 55 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.150087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.115010 restraints weight = 10389.051| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.53 r_work: 0.3277 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8294 Z= 0.205 Angle : 0.510 9.486 11251 Z= 0.269 Chirality : 0.041 0.142 1266 Planarity : 0.004 0.051 1429 Dihedral : 4.052 17.925 1190 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.54 % Allowed : 18.15 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.27), residues: 1021 helix: 2.38 (0.25), residues: 399 sheet: -0.07 (0.32), residues: 221 loop : -0.43 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.004 0.001 HIS R 63 PHE 0.011 0.001 PHE R 91 TYR 0.024 0.001 TYR N 60 ARG 0.005 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7161 (pm20) cc_final: 0.6853 (pm20) REVERT: A 15 ASP cc_start: 0.7794 (m-30) cc_final: 0.7412 (m-30) REVERT: A 131 ASN cc_start: 0.9113 (t0) cc_final: 0.8885 (t0) REVERT: A 151 GLU cc_start: 0.8210 (tp30) cc_final: 0.7805 (tp30) REVERT: B 75 GLN cc_start: 0.8308 (tt0) cc_final: 0.8059 (tt0) REVERT: B 134 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6741 (ptm160) REVERT: B 155 ASN cc_start: 0.8156 (t0) cc_final: 0.7897 (t0) REVERT: B 325 MET cc_start: 0.8500 (tpp) cc_final: 0.7972 (mmm) REVERT: N 43 LYS cc_start: 0.7971 (mtpt) cc_final: 0.7746 (mtpp) REVERT: N 53 GLN cc_start: 0.8536 (mp10) cc_final: 0.8101 (mp10) REVERT: R 90 TYR cc_start: 0.7530 (m-10) cc_final: 0.7324 (m-10) REVERT: R 262 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.7907 (mp) REVERT: R 302 MET cc_start: 0.8349 (mtt) cc_final: 0.7965 (mtp) outliers start: 22 outliers final: 12 residues processed: 159 average time/residue: 1.1459 time to fit residues: 193.6290 Evaluate side-chains 157 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 226 ASP Chi-restraints excluded: chain R residue 262 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 2 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 44 GLN B 88 ASN B 237 ASN B 259 GLN N 39 GLN N 77 ASN R 53 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.149095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.113915 restraints weight = 10427.362| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.53 r_work: 0.3259 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8294 Z= 0.250 Angle : 0.528 9.366 11251 Z= 0.278 Chirality : 0.042 0.141 1266 Planarity : 0.004 0.050 1429 Dihedral : 4.106 17.877 1190 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.31 % Allowed : 18.73 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.26), residues: 1021 helix: 2.33 (0.25), residues: 399 sheet: -0.12 (0.32), residues: 222 loop : -0.45 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.004 0.001 HIS R 63 PHE 0.014 0.001 PHE R 91 TYR 0.014 0.002 TYR N 60 ARG 0.008 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7131 (pm20) cc_final: 0.6797 (pm20) REVERT: A 15 ASP cc_start: 0.7800 (m-30) cc_final: 0.7436 (m-30) REVERT: A 131 ASN cc_start: 0.9117 (t0) cc_final: 0.8893 (t0) REVERT: A 151 GLU cc_start: 0.8202 (tp30) cc_final: 0.7805 (tp30) REVERT: B 75 GLN cc_start: 0.8304 (tt0) cc_final: 0.8043 (tt0) REVERT: B 134 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6764 (ptm160) REVERT: B 155 ASN cc_start: 0.8135 (t0) cc_final: 0.7868 (t0) REVERT: B 219 ARG cc_start: 0.8333 (mtt-85) cc_final: 0.7896 (mtp85) REVERT: B 262 MET cc_start: 0.8361 (tpt) cc_final: 0.8119 (tpp) REVERT: B 325 MET cc_start: 0.8510 (tpp) cc_final: 0.7971 (mmm) REVERT: N 53 GLN cc_start: 0.8531 (mp10) cc_final: 0.8081 (mp10) REVERT: R 262 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7892 (mp) REVERT: R 302 MET cc_start: 0.8344 (mtt) cc_final: 0.7982 (mtp) outliers start: 20 outliers final: 11 residues processed: 156 average time/residue: 1.2278 time to fit residues: 203.3435 Evaluate side-chains 151 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 226 ASP Chi-restraints excluded: chain R residue 262 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 38 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 44 GLN B 259 GLN N 77 ASN R 53 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.149720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.114537 restraints weight = 10537.707| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.55 r_work: 0.3269 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8294 Z= 0.219 Angle : 0.527 9.420 11251 Z= 0.278 Chirality : 0.041 0.139 1266 Planarity : 0.004 0.049 1429 Dihedral : 4.078 17.991 1190 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.66 % Allowed : 18.96 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.26), residues: 1021 helix: 2.37 (0.25), residues: 399 sheet: -0.14 (0.31), residues: 221 loop : -0.44 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.004 0.001 HIS R 63 PHE 0.011 0.001 PHE A 74 TYR 0.027 0.002 TYR N 60 ARG 0.008 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7126 (pm20) cc_final: 0.6790 (pm20) REVERT: A 15 ASP cc_start: 0.7812 (m-30) cc_final: 0.7459 (m-30) REVERT: A 21 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7534 (ttt180) REVERT: A 131 ASN cc_start: 0.9121 (t0) cc_final: 0.8890 (t0) REVERT: A 151 GLU cc_start: 0.8211 (tp30) cc_final: 0.7816 (tp30) REVERT: B 59 TYR cc_start: 0.8665 (m-80) cc_final: 0.8298 (m-80) REVERT: B 75 GLN cc_start: 0.8290 (tt0) cc_final: 0.8052 (tt0) REVERT: B 134 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6746 (ptm160) REVERT: B 155 ASN cc_start: 0.8167 (t0) cc_final: 0.7909 (t0) REVERT: B 219 ARG cc_start: 0.8303 (mtt-85) cc_final: 0.7884 (mtp85) REVERT: B 325 MET cc_start: 0.8497 (tpp) cc_final: 0.7956 (mmm) REVERT: N 43 LYS cc_start: 0.7958 (mtpt) cc_final: 0.7735 (mtpp) REVERT: N 53 GLN cc_start: 0.8529 (mp10) cc_final: 0.8120 (mp10) REVERT: R 262 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.7903 (mp) REVERT: R 302 MET cc_start: 0.8345 (mtt) cc_final: 0.7986 (mtp) outliers start: 23 outliers final: 15 residues processed: 160 average time/residue: 1.2142 time to fit residues: 205.8131 Evaluate side-chains 161 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 226 ASP Chi-restraints excluded: chain R residue 262 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 9 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 44 GLN B 237 ASN B 259 GLN N 77 ASN R 53 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.149893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.114950 restraints weight = 10615.206| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.54 r_work: 0.3273 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8294 Z= 0.198 Angle : 0.524 9.366 11251 Z= 0.276 Chirality : 0.041 0.141 1266 Planarity : 0.004 0.050 1429 Dihedral : 4.060 18.075 1190 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.43 % Allowed : 19.88 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.26), residues: 1021 helix: 2.30 (0.25), residues: 398 sheet: -0.05 (0.32), residues: 216 loop : -0.47 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS R 63 PHE 0.018 0.001 PHE R 91 TYR 0.014 0.001 TYR N 60 ARG 0.007 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7118 (pm20) cc_final: 0.6781 (pm20) REVERT: A 15 ASP cc_start: 0.7817 (m-30) cc_final: 0.7461 (m-30) REVERT: A 131 ASN cc_start: 0.9121 (t0) cc_final: 0.8890 (t0) REVERT: A 151 GLU cc_start: 0.8195 (tp30) cc_final: 0.7773 (tp30) REVERT: A 169 ARG cc_start: 0.8556 (mtm110) cc_final: 0.8158 (ptp90) REVERT: B 75 GLN cc_start: 0.8287 (tt0) cc_final: 0.8040 (tt0) REVERT: B 134 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6700 (ptm160) REVERT: B 155 ASN cc_start: 0.8164 (t0) cc_final: 0.7912 (t0) REVERT: B 325 MET cc_start: 0.8497 (tpp) cc_final: 0.7959 (mmm) REVERT: N 43 LYS cc_start: 0.7958 (mtpt) cc_final: 0.7735 (mtpp) REVERT: N 53 GLN cc_start: 0.8552 (mp10) cc_final: 0.8091 (mp10) REVERT: R 262 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.7890 (mp) REVERT: R 302 MET cc_start: 0.8340 (mtt) cc_final: 0.7986 (mtp) outliers start: 21 outliers final: 14 residues processed: 154 average time/residue: 1.2050 time to fit residues: 196.8314 Evaluate side-chains 154 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 226 ASP Chi-restraints excluded: chain R residue 262 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 84 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 91 optimal weight: 0.0980 chunk 90 optimal weight: 1.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 44 GLN B 259 GLN N 77 ASN R 53 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.150310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.115614 restraints weight = 10423.607| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.53 r_work: 0.3281 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8294 Z= 0.192 Angle : 0.517 9.069 11251 Z= 0.272 Chirality : 0.040 0.141 1266 Planarity : 0.004 0.052 1429 Dihedral : 4.014 18.195 1190 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.08 % Allowed : 19.77 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.26), residues: 1021 helix: 2.35 (0.25), residues: 398 sheet: -0.01 (0.32), residues: 215 loop : -0.48 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS R 63 PHE 0.010 0.001 PHE A 74 TYR 0.022 0.002 TYR N 60 ARG 0.007 0.000 ARG A 199 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7108 (pm20) cc_final: 0.6768 (pm20) REVERT: A 15 ASP cc_start: 0.7818 (m-30) cc_final: 0.7461 (m-30) REVERT: A 131 ASN cc_start: 0.9113 (t0) cc_final: 0.8882 (t0) REVERT: A 151 GLU cc_start: 0.8176 (tp30) cc_final: 0.7812 (tp30) REVERT: A 169 ARG cc_start: 0.8560 (mtm110) cc_final: 0.8144 (ptp90) REVERT: B 59 TYR cc_start: 0.8668 (m-80) cc_final: 0.8298 (m-80) REVERT: B 75 GLN cc_start: 0.8293 (tt0) cc_final: 0.8041 (tt0) REVERT: B 134 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6681 (ptm160) REVERT: B 155 ASN cc_start: 0.8162 (t0) cc_final: 0.7909 (t0) REVERT: B 219 ARG cc_start: 0.8310 (mtt-85) cc_final: 0.7877 (mtp85) REVERT: B 325 MET cc_start: 0.8512 (tpp) cc_final: 0.7978 (mmm) REVERT: N 43 LYS cc_start: 0.7942 (mtpt) cc_final: 0.7718 (mtpp) REVERT: N 53 GLN cc_start: 0.8534 (mp10) cc_final: 0.8069 (mp10) REVERT: N 59 SER cc_start: 0.8519 (OUTLIER) cc_final: 0.8227 (p) REVERT: R 262 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.7894 (mp) REVERT: R 302 MET cc_start: 0.8339 (mtt) cc_final: 0.7985 (mtp) outliers start: 18 outliers final: 11 residues processed: 152 average time/residue: 1.1641 time to fit residues: 188.2845 Evaluate side-chains 153 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 226 ASP Chi-restraints excluded: chain R residue 262 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 4 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 0.0980 chunk 12 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 44 GLN B 259 GLN N 77 ASN R 53 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.150643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.115841 restraints weight = 10509.690| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.54 r_work: 0.3285 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8294 Z= 0.186 Angle : 0.517 9.250 11251 Z= 0.272 Chirality : 0.040 0.141 1266 Planarity : 0.004 0.052 1429 Dihedral : 3.978 18.118 1190 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.62 % Allowed : 20.81 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.26), residues: 1021 helix: 2.47 (0.25), residues: 392 sheet: -0.04 (0.32), residues: 216 loop : -0.52 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS R 63 PHE 0.021 0.001 PHE R 91 TYR 0.024 0.001 TYR R 172 ARG 0.008 0.000 ARG A 199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7084.30 seconds wall clock time: 122 minutes 36.67 seconds (7356.67 seconds total)