Starting phenix.real_space_refine on Tue Mar 3 16:16:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ld4_23281/03_2026/7ld4_23281.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ld4_23281/03_2026/7ld4_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ld4_23281/03_2026/7ld4_23281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ld4_23281/03_2026/7ld4_23281.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ld4_23281/03_2026/7ld4_23281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ld4_23281/03_2026/7ld4_23281.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.76, per 1000 atoms: 0.25 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: 0.45 Conformation dependent library (CDL) restraints added in 207.8 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: 0.15 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: 0.89 Time building geometry restraints manager: 0.58 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: 9554 4.13 - 8.25: 83 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: 284 32.87 - 49.31: 62 49.31 - 65.75: 10 65.75 - 82.18: 5 Dihedral angle restraints: 4265 sinusoidal: 1678 harmonic: 2587 Sorted by residual: 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 dihedral pdb=" CA TRP B 339 " pdb=" C TRP B 339 " pdb=" N ASN B 340 " pdb=" CA ASN B 340 " ideal model delta harmonic sigma weight residual 180.00 160.65 19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 161.87 18.13 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 4262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 917 0.088 - 0.176: 179 0.176 - 0.264: 16 0.264 - 0.352: 4 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: 0.510 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.980 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.850 ------------------------------------------------------------------------------- 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 7124 Z= 0.351 Angle : 1.122 20.629 9652 Z= 0.614 Chirality : 0.070 0.440 1117 Planarity : 0.008 0.052 1206 Dihedral : 12.652 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.020 0.001 ARG R 208 TYR 0.038 0.004 TYR R 179 PHE 0.070 0.004 PHE R 275 TRP 0.022 0.003 TRP R 247 HIS 0.011 0.002 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00821 ( 7122) covalent geometry : angle 1.12111 ( 9648) SS BOND : bond 0.02271 ( 2) SS BOND : angle 2.76574 ( 4) hydrogen bonds : bond 0.25891 ( 359) hydrogen bonds : angle 7.59914 ( 1050) *********************** 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 : 0.272 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: 0.7978 (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: 0.7842 (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: 0.1175 time to fit residues: 21.6886 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 : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 74 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: 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 = 0.3887 r_free = 0.3887 target = 0.158967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.140454 restraints weight = 8574.756| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.43 r_work: 0.3545 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7124 Z= 0.142 Angle : 0.587 9.441 9652 Z= 0.314 Chirality : 0.044 0.228 1117 Planarity : 0.005 0.045 1206 Dihedral : 5.771 52.046 970 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.19 % Allowed : 10.45 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.28), residues: 871 helix: 0.56 (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 ARG 0.006 0.001 ARG R 291 TYR 0.014 0.001 TYR A 297 PHE 0.037 0.002 PHE R 275 TRP 0.020 0.002 TRP B 82 HIS 0.004 0.001 HIS R 251 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 7122) covalent geometry : angle 0.58665 ( 9648) SS BOND : bond 0.01110 ( 2) SS BOND : angle 0.69059 ( 4) hydrogen bonds : bond 0.05064 ( 359) hydrogen bonds : angle 4.70892 ( 1050) *********************** 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 146 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8185 (ttpp) cc_final: 0.7951 (tttp) REVERT: A 28 GLU cc_start: 0.7622 (pp20) cc_final: 0.7368 (pp20) REVERT: A 264 SER cc_start: 0.8919 (p) cc_final: 0.8508 (m) REVERT: B 120 ILE cc_start: 0.9222 (mm) cc_final: 0.8997 (mm) REVERT: R 162 MET cc_start: 0.6332 (mmt) cc_final: 0.5558 (mmt) outliers start: 9 outliers final: 4 residues processed: 145 average time/residue: 0.0999 time to fit residues: 18.0448 Evaluate side-chains 115 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 331 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 76 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.152047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.134318 restraints weight = 8533.564| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.35 r_work: 0.3456 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7124 Z= 0.124 Angle : 0.525 7.990 9652 Z= 0.281 Chirality : 0.042 0.218 1117 Planarity : 0.004 0.043 1206 Dihedral : 5.487 52.633 970 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.59 % Allowed : 12.57 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.28), residues: 871 helix: 0.96 (0.26), residues: 431 sheet: 0.66 (0.39), residues: 169 loop : -0.50 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.014 0.001 TYR R 288 PHE 0.026 0.001 PHE R 275 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7122) covalent geometry : angle 0.52534 ( 9648) SS BOND : bond 0.00977 ( 2) SS BOND : angle 0.54390 ( 4) hydrogen bonds : bond 0.04348 ( 359) hydrogen bonds : angle 4.35288 ( 1050) *********************** 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: 12 poor density : 120 time to evaluate : 0.263 Fit side-chains REVERT: A 21 LYS cc_start: 0.8212 (ttpp) cc_final: 0.7975 (tttp) REVERT: A 264 SER cc_start: 0.8866 (p) cc_final: 0.8452 (m) REVERT: B 120 ILE cc_start: 0.9261 (mm) cc_final: 0.9009 (mm) REVERT: B 258 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7715 (m-30) REVERT: B 333 ASP cc_start: 0.8578 (p0) cc_final: 0.8177 (p0) REVERT: G 40 TYR cc_start: 0.8609 (t80) cc_final: 0.8234 (t80) REVERT: R 162 MET cc_start: 0.6191 (mmt) cc_final: 0.5390 (mmt) REVERT: R 275 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7885 (p90) outliers start: 12 outliers final: 6 residues processed: 128 average time/residue: 0.0929 time to fit residues: 15.3146 Evaluate side-chains 114 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 306 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 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 36 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 57 optimal weight: 0.1980 chunk 28 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.152155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.134485 restraints weight = 8696.505| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.36 r_work: 0.3459 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7124 Z= 0.111 Angle : 0.503 6.077 9652 Z= 0.269 Chirality : 0.041 0.215 1117 Planarity : 0.004 0.043 1206 Dihedral : 5.280 52.521 970 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.85 % Allowed : 13.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.29), residues: 871 helix: 1.20 (0.26), residues: 430 sheet: 0.55 (0.38), residues: 175 loop : -0.48 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 291 TYR 0.013 0.001 TYR R 288 PHE 0.023 0.001 PHE R 275 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 7122) covalent geometry : angle 0.50282 ( 9648) SS BOND : bond 0.00862 ( 2) SS BOND : angle 0.48620 ( 4) hydrogen bonds : bond 0.03781 ( 359) hydrogen bonds : angle 4.19093 ( 1050) *********************** 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 125 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.203 Fit side-chains REVERT: B 120 ILE cc_start: 0.9271 (mm) cc_final: 0.9009 (mm) REVERT: B 333 ASP cc_start: 0.8546 (p0) cc_final: 0.8260 (p0) REVERT: G 40 TYR cc_start: 0.8599 (t80) cc_final: 0.8324 (t80) REVERT: R 162 MET cc_start: 0.6123 (mmt) cc_final: 0.5310 (mmt) REVERT: R 275 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7697 (p90) outliers start: 14 outliers final: 9 residues processed: 122 average time/residue: 0.1027 time to fit residues: 16.0928 Evaluate side-chains 115 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 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 84 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 0.0980 chunk 20 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN R 264 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.149833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.132258 restraints weight = 8628.444| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.34 r_work: 0.3425 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7124 Z= 0.117 Angle : 0.500 5.981 9652 Z= 0.265 Chirality : 0.042 0.231 1117 Planarity : 0.004 0.041 1206 Dihedral : 5.240 53.198 970 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.98 % Allowed : 14.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.29), residues: 871 helix: 1.42 (0.26), residues: 424 sheet: 0.49 (0.38), residues: 176 loop : -0.48 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 291 TYR 0.009 0.001 TYR R 288 PHE 0.021 0.001 PHE R 275 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 7122) covalent geometry : angle 0.50046 ( 9648) SS BOND : bond 0.00921 ( 2) SS BOND : angle 0.56277 ( 4) hydrogen bonds : bond 0.03693 ( 359) hydrogen bonds : angle 4.10884 ( 1050) *********************** 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: 15 poor density : 105 time to evaluate : 0.285 Fit side-chains REVERT: A 241 MET cc_start: 0.2851 (tpt) cc_final: 0.2422 (tpt) REVERT: B 120 ILE cc_start: 0.9283 (mm) cc_final: 0.9006 (mm) REVERT: B 258 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7818 (m-30) REVERT: B 333 ASP cc_start: 0.8421 (p0) cc_final: 0.8218 (p0) REVERT: G 40 TYR cc_start: 0.8622 (t80) cc_final: 0.8358 (t80) REVERT: R 162 MET cc_start: 0.6139 (mmt) cc_final: 0.5280 (mmt) REVERT: R 275 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7611 (p90) REVERT: R 288 TYR cc_start: 0.9286 (m-80) cc_final: 0.9055 (m-80) outliers start: 15 outliers final: 11 residues processed: 118 average time/residue: 0.1009 time to fit residues: 15.4260 Evaluate side-chains 114 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 B residue 327 VAL 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 47 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 72 optimal weight: 0.0010 chunk 13 optimal weight: 0.0070 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 overall best weight: 0.4404 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.151875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.134154 restraints weight = 8566.159| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.34 r_work: 0.3475 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7124 Z= 0.101 Angle : 0.496 8.514 9652 Z= 0.260 Chirality : 0.041 0.237 1117 Planarity : 0.004 0.044 1206 Dihedral : 5.068 51.781 970 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.78 % Allowed : 14.15 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.29), residues: 871 helix: 1.53 (0.26), residues: 423 sheet: 0.53 (0.39), residues: 175 loop : -0.43 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 291 TYR 0.008 0.001 TYR R 288 PHE 0.019 0.001 PHE R 275 TRP 0.016 0.001 TRP B 82 HIS 0.002 0.000 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 7122) covalent geometry : angle 0.49645 ( 9648) SS BOND : bond 0.00734 ( 2) SS BOND : angle 0.41073 ( 4) hydrogen bonds : bond 0.03323 ( 359) hydrogen bonds : angle 4.06157 ( 1050) *********************** 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 136 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.386 Fit side-chains REVERT: A 241 MET cc_start: 0.2867 (tpt) cc_final: 0.2486 (tpt) REVERT: A 299 GLU cc_start: 0.7977 (tp30) cc_final: 0.7696 (tp30) REVERT: B 120 ILE cc_start: 0.9255 (mm) cc_final: 0.8974 (mm) REVERT: B 234 PHE cc_start: 0.9159 (OUTLIER) cc_final: 0.8212 (m-80) REVERT: B 258 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7779 (m-30) REVERT: G 40 TYR cc_start: 0.8557 (t80) cc_final: 0.8342 (t80) REVERT: R 162 MET cc_start: 0.6170 (mmt) cc_final: 0.5413 (mmt) REVERT: R 275 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7405 (p90) outliers start: 21 outliers final: 13 residues processed: 132 average time/residue: 0.1043 time to fit residues: 17.6993 Evaluate side-chains 119 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 284 LEU 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 243 THR Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 30 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 3 optimal weight: 0.2980 chunk 13 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.153236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.135772 restraints weight = 8646.446| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.30 r_work: 0.3464 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7124 Z= 0.114 Angle : 0.527 9.172 9652 Z= 0.272 Chirality : 0.042 0.253 1117 Planarity : 0.004 0.046 1206 Dihedral : 5.140 52.903 970 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.38 % Allowed : 15.34 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.29), residues: 871 helix: 1.62 (0.26), residues: 421 sheet: 0.48 (0.38), residues: 175 loop : -0.44 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 68 TYR 0.007 0.001 TYR R 288 PHE 0.019 0.001 PHE R 275 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 7122) covalent geometry : angle 0.52705 ( 9648) SS BOND : bond 0.00844 ( 2) SS BOND : angle 0.52413 ( 4) hydrogen bonds : bond 0.03391 ( 359) hydrogen bonds : angle 4.05209 ( 1050) *********************** 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 121 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.254 Fit side-chains REVERT: A 241 MET cc_start: 0.2740 (tpt) cc_final: 0.2419 (tpt) REVERT: B 120 ILE cc_start: 0.9254 (mm) cc_final: 0.8977 (mm) REVERT: B 234 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8217 (m-80) REVERT: B 258 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.7835 (m-30) REVERT: R 162 MET cc_start: 0.6257 (mmt) cc_final: 0.5499 (mmt) REVERT: R 275 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7387 (p90) outliers start: 18 outliers final: 15 residues processed: 117 average time/residue: 0.1026 time to fit residues: 15.4832 Evaluate side-chains 119 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 279 ILE 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 234 PHE Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR 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 41 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 77 optimal weight: 0.1980 chunk 42 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 75 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.151264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.133203 restraints weight = 8629.730| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.36 r_work: 0.3444 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7124 Z= 0.114 Angle : 0.525 9.836 9652 Z= 0.271 Chirality : 0.041 0.259 1117 Planarity : 0.004 0.043 1206 Dihedral : 5.127 52.993 970 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.04 % Allowed : 14.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.29), residues: 871 helix: 1.64 (0.26), residues: 421 sheet: 0.48 (0.38), residues: 175 loop : -0.42 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 68 TYR 0.007 0.001 TYR R 288 PHE 0.019 0.001 PHE R 275 TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS R 251 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 7122) covalent geometry : angle 0.52539 ( 9648) SS BOND : bond 0.00832 ( 2) SS BOND : angle 0.52943 ( 4) hydrogen bonds : bond 0.03356 ( 359) hydrogen bonds : angle 4.02975 ( 1050) *********************** 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 132 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.264 Fit side-chains REVERT: A 241 MET cc_start: 0.2914 (tpt) cc_final: 0.2555 (tpt) REVERT: A 249 LYS cc_start: 0.7918 (mmmt) cc_final: 0.7490 (mmtm) REVERT: B 120 ILE cc_start: 0.9253 (mm) cc_final: 0.8973 (mm) REVERT: B 234 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8292 (m-80) REVERT: B 258 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7800 (m-30) REVERT: G 28 ILE cc_start: 0.8264 (mt) cc_final: 0.8027 (mt) REVERT: R 162 MET cc_start: 0.6295 (mmt) cc_final: 0.5531 (mmt) REVERT: R 275 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7314 (p90) outliers start: 23 outliers final: 15 residues processed: 126 average time/residue: 0.0954 time to fit residues: 15.5770 Evaluate side-chains 122 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 342 ASP 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 B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 59 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.149555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.132521 restraints weight = 8534.462| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.21 r_work: 0.3421 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7124 Z= 0.129 Angle : 0.547 9.851 9652 Z= 0.284 Chirality : 0.042 0.266 1117 Planarity : 0.004 0.041 1206 Dihedral : 5.226 53.866 970 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.51 % Allowed : 15.74 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.28), residues: 871 helix: 1.61 (0.26), residues: 423 sheet: 0.50 (0.38), residues: 168 loop : -0.52 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 68 TYR 0.015 0.001 TYR G 40 PHE 0.020 0.001 PHE R 275 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS R 251 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7122) covalent geometry : angle 0.54653 ( 9648) SS BOND : bond 0.00930 ( 2) SS BOND : angle 0.58293 ( 4) hydrogen bonds : bond 0.03563 ( 359) hydrogen bonds : angle 4.06471 ( 1050) *********************** 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 123 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.285 Fit side-chains REVERT: A 241 MET cc_start: 0.3130 (tpt) cc_final: 0.2782 (tpt) REVERT: A 299 GLU cc_start: 0.7967 (tp30) cc_final: 0.7701 (tp30) REVERT: B 120 ILE cc_start: 0.9224 (mm) cc_final: 0.8928 (mm) REVERT: B 258 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7878 (m-30) REVERT: R 162 MET cc_start: 0.6281 (mmt) cc_final: 0.5596 (mmt) REVERT: R 275 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7343 (p90) outliers start: 19 outliers final: 16 residues processed: 118 average time/residue: 0.1047 time to fit residues: 16.0243 Evaluate side-chains 121 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 342 ASP 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 258 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR 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 62 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 chunk 54 optimal weight: 0.0020 chunk 21 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 overall best weight: 0.9590 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.149066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.132740 restraints weight = 8493.526| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.23 r_work: 0.3441 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7124 Z= 0.132 Angle : 0.555 10.324 9652 Z= 0.288 Chirality : 0.042 0.256 1117 Planarity : 0.004 0.042 1206 Dihedral : 5.269 54.110 970 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.65 % Allowed : 15.48 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.28), residues: 871 helix: 1.61 (0.26), residues: 422 sheet: 0.42 (0.38), residues: 168 loop : -0.53 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 68 TYR 0.012 0.001 TYR B 264 PHE 0.020 0.001 PHE R 275 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS R 251 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 7122) covalent geometry : angle 0.55521 ( 9648) SS BOND : bond 0.00966 ( 2) SS BOND : angle 0.63916 ( 4) hydrogen bonds : bond 0.03579 ( 359) hydrogen bonds : angle 4.08369 ( 1050) ********************** 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 123 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.278 Fit side-chains REVERT: A 241 MET cc_start: 0.3196 (tpt) cc_final: 0.2886 (tpt) REVERT: B 18 ILE cc_start: 0.8229 (mt) cc_final: 0.7998 (mt) REVERT: B 120 ILE cc_start: 0.9212 (mm) cc_final: 0.8928 (mm) REVERT: B 234 PHE cc_start: 0.9133 (OUTLIER) cc_final: 0.8376 (m-80) REVERT: B 258 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.7918 (m-30) REVERT: G 62 ARG cc_start: 0.6931 (mmp-170) cc_final: 0.6703 (mmt180) REVERT: R 162 MET cc_start: 0.6299 (mmt) cc_final: 0.5586 (mmt) REVERT: R 275 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7314 (p90) outliers start: 20 outliers final: 16 residues processed: 118 average time/residue: 0.0939 time to fit residues: 14.3478 Evaluate side-chains 118 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 342 ASP 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 B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR 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 80 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 58 optimal weight: 0.0020 chunk 83 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.150190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.133232 restraints weight = 8424.482| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.19 r_work: 0.3443 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7124 Z= 0.120 Angle : 0.552 9.999 9652 Z= 0.285 Chirality : 0.042 0.253 1117 Planarity : 0.004 0.041 1206 Dihedral : 5.202 53.622 970 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.78 % Allowed : 15.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.28), residues: 871 helix: 1.61 (0.26), residues: 423 sheet: 0.45 (0.38), residues: 168 loop : -0.54 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 68 TYR 0.017 0.001 TYR G 40 PHE 0.019 0.001 PHE R 275 TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS R 251 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7122) covalent geometry : angle 0.55194 ( 9648) SS BOND : bond 0.00859 ( 2) SS BOND : angle 0.54333 ( 4) hydrogen bonds : bond 0.03484 ( 359) hydrogen bonds : angle 4.05305 ( 1050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1759.04 seconds wall clock time: 30 minutes 48.30 seconds (1848.30 seconds total)