Starting phenix.real_space_refine on Wed Mar 12 01:09:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ld4_23281/03_2025/7ld4_23281.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ld4_23281/03_2025/7ld4_23281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ld4_23281/03_2025/7ld4_23281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ld4_23281/03_2025/7ld4_23281.map" model { file = "/net/cci-nas-00/data/ceres_data/7ld4_23281/03_2025/7ld4_23281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ld4_23281/03_2025/7ld4_23281.cif" } resolution = 3.3 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= 0.004 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 52 5.16 5 C 4476 2.51 5 N 1187 2.21 5 O 1266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 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: 6981 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1693 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 207} Chain breaks: 2 Chain: "B" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2568 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Chain: "G" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "R" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2267 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 14, 'TRANS': 272} Chain breaks: 1 Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {'ADN%rna2p': 1} Classifications: {'undetermined': 1, 'water': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Time building chain proxies: 4.79, per 1000 atoms: 0.69 Number of scatterers: 6981 At special positions: 0 Unit cell: (82.68, 125.08, 90.1, 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 52 16.00 O 1266 8.00 N 1187 7.00 C 4476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 80 " - pdb=" SG CYS R 169 " distance=2.00 Simple disulfide: pdb=" SG CYS R 260 " - pdb=" SG CYS R 263 " 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: 1.48 Conformation dependent library (CDL) restraints added in 905.6 milliseconds 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1682 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 9 sheets defined 47.8% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 11 through 30 removed outlier: 3.632A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 4.192A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.507A pdb=" N LYS A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 217 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 removed outlier: 4.402A pdb=" N ASP A 232 " --> pdb=" O SER A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 242 through 256 removed outlier: 3.500A pdb=" N ASN A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 279 Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 328 through 353 removed outlier: 4.017A pdb=" N ASN A 332 " --> pdb=" O THR A 328 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.588A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.884A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.521A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'R' and resid 6 through 37 Proline residue: R 25 - end of helix removed outlier: 3.668A pdb=" N ASN R 37 " --> pdb=" O ALA R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 61 removed outlier: 3.593A pdb=" N PHE R 47 " --> pdb=" O ALA R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 72 Processing helix chain 'R' and resid 77 through 111 Proline residue: R 86 - end of helix removed outlier: 4.201A pdb=" N VAL R 109 " --> pdb=" O ARG R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 119 Processing helix chain 'R' and resid 120 through 141 removed outlier: 3.540A pdb=" N VAL R 126 " --> pdb=" O ARG R 122 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL R 138 " --> pdb=" O LEU R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 160 removed outlier: 3.698A pdb=" N ARG R 154 " --> pdb=" O SER R 150 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN R 159 " --> pdb=" O ALA R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 175 Processing helix chain 'R' and resid 176 through 183 removed outlier: 3.520A pdb=" N MET R 180 " --> pdb=" O SER R 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 184 through 189 Processing helix chain 'R' and resid 189 through 213 Processing helix chain 'R' and resid 225 through 259 removed outlier: 3.979A pdb=" N LEU R 248 " --> pdb=" O ALA R 244 " (cutoff:3.500A) Proline residue: R 249 - end of helix Processing helix chain 'R' and resid 266 through 288 removed outlier: 3.773A pdb=" N THR R 270 " --> pdb=" O PRO R 266 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N SER R 281 " --> pdb=" O THR R 277 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA R 282 " --> pdb=" O HIS R 278 " (cutoff:3.500A) Proline residue: R 285 - end of helix Processing helix chain 'R' and resid 292 through 301 removed outlier: 3.679A pdb=" N THR R 298 " --> pdb=" O LYS R 294 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE R 299 " --> pdb=" O PHE R 295 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 192 removed outlier: 8.966A pdb=" N ALA A 221 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N ALA A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.432A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.533A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.608A 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: 6.956A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.710A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.602A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.213A 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: 6.607A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.464A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 74 through 76 359 hydrogen bonds defined for protein. 1050 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2170 1.34 - 1.46: 1309 1.46 - 1.58: 3568 1.58 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 7122 Sorted by residual: bond pdb=" CB VAL R 62 " pdb=" CG2 VAL R 62 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.23e+00 bond pdb=" CB VAL R 119 " pdb=" CG1 VAL R 119 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.15e+00 bond pdb=" C VAL R 24 " pdb=" N PRO R 25 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.20e-02 6.94e+03 3.15e+00 bond pdb=" CB CYS A 352 " pdb=" SG CYS A 352 " ideal model delta sigma weight residual 1.808 1.750 0.058 3.30e-02 9.18e+02 3.12e+00 bond pdb=" CB VAL R 83 " pdb=" CG2 VAL R 83 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.77e+00 ... (remaining 7117 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.13: 9555 4.13 - 8.25: 82 8.25 - 12.38: 7 12.38 - 16.50: 3 16.50 - 20.63: 1 Bond angle restraints: 9648 Sorted by residual: angle pdb=" CA CYS R 169 " pdb=" CB CYS R 169 " pdb=" SG CYS R 169 " ideal model delta sigma weight residual 114.40 97.97 16.43 2.30e+00 1.89e-01 5.10e+01 angle pdb=" CA LEU R 68 " pdb=" CB LEU R 68 " pdb=" CG LEU R 68 " ideal model delta sigma weight residual 116.30 136.93 -20.63 3.50e+00 8.16e-02 3.47e+01 angle pdb=" N GLY R 72 " pdb=" CA GLY R 72 " pdb=" C GLY R 72 " ideal model delta sigma weight residual 112.34 124.06 -11.72 2.04e+00 2.40e-01 3.30e+01 angle pdb=" N VAL R 119 " pdb=" CA VAL R 119 " pdb=" C VAL R 119 " ideal model delta sigma weight residual 106.21 111.35 -5.14 1.07e+00 8.73e-01 2.31e+01 angle pdb=" CA LEU R 18 " pdb=" CB LEU R 18 " pdb=" CG LEU R 18 " ideal model delta sigma weight residual 116.30 130.57 -14.27 3.50e+00 8.16e-02 1.66e+01 ... (remaining 9643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 3904 16.44 - 32.87: 282 32.87 - 49.31: 64 49.31 - 65.75: 10 65.75 - 82.18: 5 Dihedral angle restraints: 4265 sinusoidal: 1678 harmonic: 2587 Sorted by residual: dihedral pdb=" C1' ADN R 401 " pdb=" C2' ADN R 401 " pdb=" C3' ADN R 401 " pdb=" C4' ADN R 401 " ideal model delta sinusoidal sigma weight residual -35.00 6.27 -41.27 1 8.00e+00 1.56e-02 3.73e+01 dihedral pdb=" C2' ADN R 401 " pdb=" C3' ADN R 401 " pdb=" C4' ADN R 401 " pdb=" O4' ADN R 401 " ideal model delta sinusoidal sigma weight residual 24.00 -13.82 37.82 1 8.00e+00 1.56e-02 3.15e+01 dihedral pdb=" CA THR B 249 " pdb=" C THR B 249 " pdb=" N CYS B 250 " pdb=" CA CYS B 250 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 4262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 918 0.088 - 0.176: 179 0.176 - 0.264: 16 0.264 - 0.352: 3 0.352 - 0.440: 1 Chirality restraints: 1117 Sorted by residual: chirality pdb=" CB VAL A 202 " pdb=" CA VAL A 202 " pdb=" CG1 VAL A 202 " pdb=" CG2 VAL A 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" CB VAL R 119 " pdb=" CA VAL R 119 " pdb=" CG1 VAL R 119 " pdb=" CG2 VAL R 119 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB VAL R 83 " pdb=" CA VAL R 83 " pdb=" CG1 VAL R 83 " pdb=" CG2 VAL R 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 1114 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 275 " 0.029 2.00e-02 2.50e+03 3.00e-02 1.58e+01 pdb=" CG PHE R 275 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE R 275 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE R 275 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE R 275 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 275 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE R 275 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADN R 401 " 0.010 2.00e-02 2.50e+03 2.02e-02 1.12e+01 pdb=" C2 ADN R 401 " 0.018 2.00e-02 2.50e+03 pdb=" C4 ADN R 401 " -0.033 2.00e-02 2.50e+03 pdb=" C5 ADN R 401 " -0.022 2.00e-02 2.50e+03 pdb=" C6 ADN R 401 " 0.004 2.00e-02 2.50e+03 pdb=" C8 ADN R 401 " 0.025 2.00e-02 2.50e+03 pdb=" N1 ADN R 401 " 0.029 2.00e-02 2.50e+03 pdb=" N3 ADN R 401 " -0.015 2.00e-02 2.50e+03 pdb=" N6 ADN R 401 " -0.018 2.00e-02 2.50e+03 pdb=" N7 ADN R 401 " 0.015 2.00e-02 2.50e+03 pdb=" N9 ADN R 401 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 22 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.32e+00 pdb=" C VAL R 22 " -0.050 2.00e-02 2.50e+03 pdb=" O VAL R 22 " 0.018 2.00e-02 2.50e+03 pdb=" N SER R 23 " 0.017 2.00e-02 2.50e+03 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1698 2.80 - 3.32: 6374 3.32 - 3.85: 11494 3.85 - 4.37: 13606 4.37 - 4.90: 23609 Nonbonded interactions: 56781 Sorted by model distance: nonbonded pdb=" O SER B 334 " pdb=" OG SER B 334 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.284 3.040 nonbonded pdb=" OE2 GLU A 319 " pdb=" OH TYR A 321 " model vdw 2.294 3.040 nonbonded pdb=" O SER R 23 " pdb=" ND2 ASN R 27 " model vdw 2.340 3.120 nonbonded pdb=" O LEU R 90 " pdb=" OG SER R 93 " model vdw 2.340 3.040 ... (remaining 56776 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: 0.500 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.090 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 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 : 0.008 0.075 7122 Z= 0.543 Angle : 1.119 20.629 9648 Z= 0.616 Chirality : 0.070 0.440 1117 Planarity : 0.008 0.052 1206 Dihedral : 12.683 82.182 2577 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.26 % Allowed : 4.37 % Favored : 95.37 % 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: 871 helix: -0.83 (0.24), residues: 401 sheet: 0.82 (0.40), residues: 167 loop : -0.79 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP R 247 HIS 0.011 0.002 HIS A 281 PHE 0.070 0.004 PHE R 275 TYR 0.038 0.004 TYR R 179 ARG 0.020 0.001 ARG R 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7365 (tpt-90) cc_final: 0.7091 (ttm-80) REVERT: A 21 LYS cc_start: 0.7977 (ttpp) cc_final: 0.7672 (tttp) REVERT: A 342 ASP cc_start: 0.7880 (m-30) cc_final: 0.7614 (m-30) REVERT: B 120 ILE cc_start: 0.9125 (mm) cc_final: 0.8922 (mm) REVERT: B 275 SER cc_start: 0.9031 (m) cc_final: 0.8821 (m) REVERT: R 74 GLN cc_start: 0.8331 (mt0) cc_final: 0.8036 (mp10) REVERT: R 76 TYR cc_start: 0.8135 (m-80) cc_final: 0.7843 (m-10) REVERT: R 162 MET cc_start: 0.6158 (mmt) cc_final: 0.5497 (mmt) REVERT: R 234 LYS cc_start: 0.7650 (mtpt) cc_final: 0.6674 (tttp) REVERT: R 288 TYR cc_start: 0.9280 (m-80) cc_final: 0.9001 (m-80) outliers start: 2 outliers final: 0 residues processed: 151 average time/residue: 0.2887 time to fit residues: 53.4560 Evaluate side-chains 112 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN A 295 ASN B 17 GLN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.158666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.140188 restraints weight = 8520.023| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.43 r_work: 0.3564 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7122 Z= 0.205 Angle : 0.589 9.563 9648 Z= 0.317 Chirality : 0.044 0.227 1117 Planarity : 0.005 0.045 1206 Dihedral : 7.826 66.354 970 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.06 % Allowed : 10.71 % Favored : 88.23 % 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: 0.28 (0.28), residues: 871 helix: 0.54 (0.25), residues: 420 sheet: 0.77 (0.39), residues: 170 loop : -0.56 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 247 HIS 0.004 0.001 HIS R 251 PHE 0.037 0.002 PHE R 275 TYR 0.013 0.001 TYR A 297 ARG 0.005 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8189 (ttpp) cc_final: 0.7955 (tttp) REVERT: A 28 GLU cc_start: 0.7640 (pp20) cc_final: 0.7388 (pp20) REVERT: A 264 SER cc_start: 0.8916 (p) cc_final: 0.8506 (m) REVERT: B 120 ILE cc_start: 0.9219 (mm) cc_final: 0.8942 (mm) REVERT: B 290 ASP cc_start: 0.8301 (m-30) cc_final: 0.8086 (m-30) REVERT: R 162 MET cc_start: 0.6340 (mmt) cc_final: 0.5568 (mmt) outliers start: 8 outliers final: 3 residues processed: 142 average time/residue: 0.2509 time to fit residues: 44.6478 Evaluate side-chains 114 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain R residue 83 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 17 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 18 optimal weight: 0.0870 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 295 ASN B 230 ASN R 264 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.151701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.133211 restraints weight = 8546.709| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.40 r_work: 0.3422 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7122 Z= 0.176 Angle : 0.528 8.074 9648 Z= 0.285 Chirality : 0.042 0.215 1117 Planarity : 0.004 0.042 1206 Dihedral : 7.480 64.978 970 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.46 % Allowed : 12.30 % Favored : 86.24 % 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: 0.61 (0.28), residues: 871 helix: 0.97 (0.26), residues: 429 sheet: 0.71 (0.39), residues: 169 loop : -0.56 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS R 264 PHE 0.026 0.001 PHE R 275 TYR 0.014 0.001 TYR R 288 ARG 0.004 0.000 ARG R 291 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.732 Fit side-chains REVERT: A 21 LYS cc_start: 0.8157 (ttpp) cc_final: 0.7918 (tttp) REVERT: A 264 SER cc_start: 0.8893 (p) cc_final: 0.8478 (m) REVERT: B 120 ILE cc_start: 0.9253 (mm) cc_final: 0.9002 (mm) REVERT: B 258 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7756 (m-30) REVERT: B 333 ASP cc_start: 0.8579 (p0) cc_final: 0.8150 (p0) REVERT: R 162 MET cc_start: 0.6200 (mmt) cc_final: 0.5420 (mmt) REVERT: R 275 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7876 (p90) outliers start: 11 outliers final: 6 residues processed: 129 average time/residue: 0.2352 time to fit residues: 38.8277 Evaluate side-chains 113 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 275 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 5 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 264 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.150398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.132117 restraints weight = 8582.590| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.40 r_work: 0.3423 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7122 Z= 0.188 Angle : 0.518 6.733 9648 Z= 0.278 Chirality : 0.042 0.218 1117 Planarity : 0.004 0.044 1206 Dihedral : 7.439 65.886 970 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.12 % Allowed : 13.62 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.29), residues: 871 helix: 1.12 (0.26), residues: 431 sheet: 0.42 (0.38), residues: 177 loop : -0.47 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 264 PHE 0.024 0.001 PHE R 275 TYR 0.013 0.001 TYR R 288 ARG 0.004 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.766 Fit side-chains REVERT: B 120 ILE cc_start: 0.9264 (mm) cc_final: 0.9002 (mm) REVERT: B 258 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7804 (m-30) REVERT: B 333 ASP cc_start: 0.8540 (p0) cc_final: 0.8316 (p0) REVERT: G 40 TYR cc_start: 0.8621 (t80) cc_final: 0.8340 (t80) REVERT: R 162 MET cc_start: 0.6258 (mmt) cc_final: 0.5472 (mmt) REVERT: R 275 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7733 (p90) outliers start: 16 outliers final: 10 residues processed: 119 average time/residue: 0.2190 time to fit residues: 33.9102 Evaluate side-chains 111 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 275 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 8 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 83 optimal weight: 0.0770 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 264 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.150180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.131774 restraints weight = 8547.078| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.42 r_work: 0.3410 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7122 Z= 0.184 Angle : 0.511 6.903 9648 Z= 0.273 Chirality : 0.042 0.229 1117 Planarity : 0.004 0.041 1206 Dihedral : 7.394 66.166 970 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.85 % Allowed : 14.81 % Favored : 83.33 % 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: 0.82 (0.29), residues: 871 helix: 1.33 (0.26), residues: 424 sheet: 0.35 (0.38), residues: 181 loop : -0.46 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 264 PHE 0.022 0.001 PHE R 275 TYR 0.012 0.001 TYR R 288 ARG 0.004 0.000 ARG R 291 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.791 Fit side-chains REVERT: A 241 MET cc_start: 0.3057 (tpt) cc_final: 0.2562 (tpt) REVERT: B 120 ILE cc_start: 0.9277 (mm) cc_final: 0.9005 (mm) REVERT: B 258 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.7810 (m-30) REVERT: B 333 ASP cc_start: 0.8466 (p0) cc_final: 0.8261 (p0) REVERT: G 40 TYR cc_start: 0.8632 (t80) cc_final: 0.8382 (t80) REVERT: R 162 MET cc_start: 0.6207 (mmt) cc_final: 0.5599 (mmt) REVERT: R 275 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7685 (p90) outliers start: 14 outliers final: 11 residues processed: 118 average time/residue: 0.2344 time to fit residues: 35.5829 Evaluate side-chains 115 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 275 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 42 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 264 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.147175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.129961 restraints weight = 8517.557| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.21 r_work: 0.3395 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7122 Z= 0.224 Angle : 0.537 9.230 9648 Z= 0.283 Chirality : 0.043 0.249 1117 Planarity : 0.004 0.043 1206 Dihedral : 7.403 65.816 970 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.51 % Allowed : 15.08 % Favored : 82.41 % 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: 0.82 (0.29), residues: 871 helix: 1.35 (0.26), residues: 422 sheet: 0.30 (0.38), residues: 181 loop : -0.45 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 PHE 0.022 0.001 PHE R 275 TYR 0.009 0.001 TYR R 288 ARG 0.007 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.707 Fit side-chains REVERT: A 241 MET cc_start: 0.3196 (tpt) cc_final: 0.2816 (tpt) REVERT: A 299 GLU cc_start: 0.8085 (tp30) cc_final: 0.7773 (tp30) REVERT: B 120 ILE cc_start: 0.9221 (mm) cc_final: 0.8927 (mm) REVERT: B 258 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7823 (m-30) REVERT: G 40 TYR cc_start: 0.8643 (t80) cc_final: 0.8402 (t80) REVERT: R 162 MET cc_start: 0.6242 (mmt) cc_final: 0.5588 (mmt) REVERT: R 275 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7638 (p90) outliers start: 19 outliers final: 14 residues processed: 124 average time/residue: 0.2164 time to fit residues: 34.9286 Evaluate side-chains 121 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 275 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 81 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 2 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.149076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.131924 restraints weight = 8424.944| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.21 r_work: 0.3426 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7122 Z= 0.171 Angle : 0.522 8.646 9648 Z= 0.275 Chirality : 0.042 0.255 1117 Planarity : 0.004 0.043 1206 Dihedral : 7.335 65.999 970 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.65 % Allowed : 15.21 % Favored : 82.14 % 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: 0.89 (0.29), residues: 871 helix: 1.47 (0.26), residues: 420 sheet: 0.28 (0.38), residues: 181 loop : -0.47 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS R 251 PHE 0.020 0.001 PHE R 275 TYR 0.008 0.001 TYR G 40 ARG 0.006 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.677 Fit side-chains REVERT: A 241 MET cc_start: 0.3292 (tpt) cc_final: 0.2884 (tpt) REVERT: B 120 ILE cc_start: 0.9213 (mm) cc_final: 0.8926 (mm) REVERT: B 234 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8223 (m-80) REVERT: B 258 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7782 (m-30) REVERT: R 162 MET cc_start: 0.6285 (mmt) cc_final: 0.5604 (mmt) REVERT: R 275 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7424 (p90) outliers start: 20 outliers final: 13 residues processed: 121 average time/residue: 0.2205 time to fit residues: 34.6613 Evaluate side-chains 116 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 275 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 32 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 75 optimal weight: 0.2980 chunk 78 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.149419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.132341 restraints weight = 8561.946| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.20 r_work: 0.3424 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7122 Z= 0.176 Angle : 0.533 9.901 9648 Z= 0.278 Chirality : 0.042 0.264 1117 Planarity : 0.004 0.042 1206 Dihedral : 7.334 66.200 970 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.51 % Allowed : 15.87 % Favored : 81.61 % 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: 0.90 (0.29), residues: 871 helix: 1.52 (0.26), residues: 420 sheet: 0.25 (0.38), residues: 179 loop : -0.52 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS R 251 PHE 0.020 0.001 PHE R 275 TYR 0.009 0.001 TYR R 288 ARG 0.007 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.800 Fit side-chains REVERT: A 241 MET cc_start: 0.3238 (tpt) cc_final: 0.2880 (tpt) REVERT: B 18 ILE cc_start: 0.8298 (mt) cc_final: 0.8052 (mt) REVERT: B 120 ILE cc_start: 0.9190 (mm) cc_final: 0.8890 (mm) REVERT: B 234 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8419 (m-80) REVERT: B 258 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7895 (m-30) REVERT: B 290 ASP cc_start: 0.8052 (m-30) cc_final: 0.7734 (m-30) REVERT: B 314 ARG cc_start: 0.8679 (ttm170) cc_final: 0.8326 (ttm170) REVERT: R 162 MET cc_start: 0.6291 (mmt) cc_final: 0.5604 (mmt) REVERT: R 275 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7405 (p90) outliers start: 19 outliers final: 13 residues processed: 120 average time/residue: 0.2080 time to fit residues: 32.6314 Evaluate side-chains 120 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 275 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 76 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 75 optimal weight: 0.0270 chunk 84 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.148230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.130376 restraints weight = 8669.816| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.30 r_work: 0.3385 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7122 Z= 0.272 Angle : 0.590 9.910 9648 Z= 0.308 Chirality : 0.044 0.282 1117 Planarity : 0.004 0.044 1206 Dihedral : 7.451 64.893 970 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.65 % Allowed : 15.74 % Favored : 81.61 % 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: 0.76 (0.28), residues: 871 helix: 1.35 (0.26), residues: 421 sheet: 0.25 (0.38), residues: 173 loop : -0.53 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.004 0.001 HIS G 44 PHE 0.023 0.002 PHE R 275 TYR 0.013 0.001 TYR G 40 ARG 0.006 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.710 Fit side-chains REVERT: A 241 MET cc_start: 0.3396 (tpt) cc_final: 0.3060 (tpt) REVERT: A 299 GLU cc_start: 0.8025 (tp30) cc_final: 0.7682 (tp30) REVERT: B 120 ILE cc_start: 0.9220 (mm) cc_final: 0.8931 (mm) REVERT: B 234 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8499 (m-80) REVERT: B 258 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.8020 (m-30) REVERT: G 62 ARG cc_start: 0.7248 (mmp-170) cc_final: 0.6910 (mmt180) REVERT: R 162 MET cc_start: 0.6491 (mmt) cc_final: 0.5718 (mmt) REVERT: R 275 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7510 (p90) outliers start: 20 outliers final: 15 residues processed: 128 average time/residue: 0.2315 time to fit residues: 38.1746 Evaluate side-chains 123 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 275 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 65 optimal weight: 0.9980 chunk 73 optimal weight: 0.2980 chunk 37 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 5 optimal weight: 0.0270 chunk 35 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 9 optimal weight: 0.2980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.152795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.134354 restraints weight = 8663.563| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.38 r_work: 0.3446 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7122 Z= 0.157 Angle : 0.540 9.759 9648 Z= 0.280 Chirality : 0.041 0.255 1117 Planarity : 0.004 0.044 1206 Dihedral : 7.288 65.415 970 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.85 % Allowed : 16.80 % Favored : 81.35 % 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: 0.96 (0.29), residues: 871 helix: 1.52 (0.26), residues: 423 sheet: 0.37 (0.38), residues: 173 loop : -0.48 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.000 HIS R 264 PHE 0.018 0.001 PHE R 275 TYR 0.008 0.001 TYR G 40 ARG 0.007 0.000 ARG B 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.782 Fit side-chains REVERT: A 241 MET cc_start: 0.3239 (tpt) cc_final: 0.2865 (tpt) REVERT: B 18 ILE cc_start: 0.8064 (mt) cc_final: 0.7819 (mt) REVERT: B 120 ILE cc_start: 0.9215 (mm) cc_final: 0.8936 (mm) REVERT: B 150 ARG cc_start: 0.8718 (mmt-90) cc_final: 0.8499 (mpt180) REVERT: B 234 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8230 (m-80) REVERT: G 28 ILE cc_start: 0.8280 (mt) cc_final: 0.8040 (mt) REVERT: G 47 GLU cc_start: 0.8409 (mp0) cc_final: 0.8076 (mp0) REVERT: G 62 ARG cc_start: 0.6988 (mmp-170) cc_final: 0.6699 (mmt180) REVERT: R 162 MET cc_start: 0.6310 (mmt) cc_final: 0.5645 (mmt) REVERT: R 275 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7268 (p90) outliers start: 14 outliers final: 11 residues processed: 125 average time/residue: 0.2393 time to fit residues: 38.6239 Evaluate side-chains 119 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 275 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 81 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 chunk 7 optimal weight: 0.0370 chunk 71 optimal weight: 0.5980 chunk 77 optimal weight: 0.0980 chunk 59 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.152021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.135156 restraints weight = 8501.486| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.19 r_work: 0.3457 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7122 Z= 0.152 Angle : 0.538 9.476 9648 Z= 0.278 Chirality : 0.042 0.257 1117 Planarity : 0.004 0.044 1206 Dihedral : 7.270 66.241 970 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.25 % Allowed : 17.06 % Favored : 80.69 % 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: 1.11 (0.29), residues: 871 helix: 1.63 (0.26), residues: 424 sheet: 0.46 (0.38), residues: 173 loop : -0.40 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS R 264 PHE 0.017 0.001 PHE R 275 TYR 0.016 0.001 TYR G 40 ARG 0.007 0.000 ARG B 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3654.95 seconds wall clock time: 63 minutes 33.16 seconds (3813.16 seconds total)