Starting phenix.real_space_refine on Fri Sep 11 02:45:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ld4_23281/09_2026/7ld4_23281.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ld4_23281/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7ld4_23281/09_2026/7ld4_23281.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ld4_23281/09_2026/7ld4_23281.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ld4_23281/09_2026/7ld4_23281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ld4_23281/09_2026/7ld4_23281.map" model { file = "/net/cci-nas-00/data/ceres_data/7ld4_23281/09_2026/7ld4_23281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ld4_23281/09_2026/7ld4_23281.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 1.92, per 1000 atoms: 0.28 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: 0.53 Conformation dependent library (CDL) restraints added in 484.8 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: 0.20 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: 1.11 Time building geometry restraints manager: 0.75 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: 3898 16.44 - 32.87: 274 32.87 - 49.31: 56 49.31 - 65.75: 10 65.75 - 82.18: 5 Dihedral angle restraints: 4243 sinusoidal: 1656 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 4240 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: 0.580 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.540 Find NCS groups from input model: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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= 0.350 Angle : 1.120 20.629 9652 Z= 0.616 Chirality : 0.070 0.440 1117 Planarity : 0.008 0.052 1206 Dihedral : 12.434 82.182 2555 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/Z covalent geometry : bond 0.00820 / 0.35 ( 7122) covalent geometry : angle 1.11873 / 0.62 ( 9648) SS BOND : bond 0.02271 / 1.19 ( 2) SS BOND : angle 2.76574 / 1.84 ( 4) hydrogen bonds : bond 0.25891 / 17.23 ( 359) hydrogen bonds : angle 7.59914 / 5.25 ( 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 : 0.267 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: 0.1311 time to fit residues: 24.4658 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 : 0.262 ------------------------------------------------------------------------------- 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... A 242 ASN A 295 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.158649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.140153 restraints weight = 8573.788| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.42 r_work: 0.3566 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1983 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= 0.154 Angle : 0.592 9.646 9652 Z= 0.319 Chirality : 0.044 0.229 1117 Planarity : 0.005 0.045 1206 Dihedral : 4.757 19.707 948 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.93 % Allowed : 10.85 % 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 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: 0.28 (0.28), residues: 871 helix: 0.54 (0.25), residues: 421 sheet: 0.77 (0.39), residues: 170 loop : -0.55 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 291 TYR 0.013 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/Z covalent geometry : bond 0.00313 / 0.15 ( 7122) covalent geometry : angle 0.59220 / 0.32 ( 9648) SS BOND : bond 0.01113 / 0.59 ( 2) SS BOND : angle 0.65408 / 0.40 ( 4) hydrogen bonds : bond 0.05334 / 3.42 ( 359) hydrogen bonds : angle 4.75493 / 3.30 ( 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 143 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 0.217 Fit side-chains REVERT: A 21 LYS cc_start: 0.8180 (ttpp) cc_final: 0.7946 (tttp) REVERT: A 28 GLU cc_start: 0.7645 (pp20) cc_final: 0.7394 (pp20) REVERT: A 264 SER cc_start: 0.8913 (p) cc_final: 0.8506 (m) REVERT: B 120 ILE cc_start: 0.9216 (mm) cc_final: 0.8937 (mm) REVERT: B 290 ASP cc_start: 0.8299 (m-30) cc_final: 0.8081 (m-30) REVERT: R 162 MET cc_start: 0.6277 (mmt) cc_final: 0.5561 (mmt) outliers start: 7 outliers final: 4 residues processed: 142 average time/residue: 0.1151 time to fit residues: 20.6646 Evaluate side-chains 113 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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: 0.9990 chunk 14 optimal weight: 0.0870 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 HIS A 295 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 264 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.148390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.130764 restraints weight = 8612.105| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.35 r_work: 0.3363 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7124 Z= 0.179 Angle : 0.572 8.362 9652 Z= 0.307 Chirality : 0.044 0.227 1117 Planarity : 0.005 0.046 1206 Dihedral : 4.547 18.027 948 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.85 % Allowed : 13.10 % Favored : 85.05 % 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: 0.47 (0.28), residues: 871 helix: 0.84 (0.26), residues: 427 sheet: 0.57 (0.39), residues: 169 loop : -0.54 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 68 TYR 0.014 0.001 TYR R 288 PHE 0.028 0.002 PHE R 275 TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 7122) covalent geometry : angle 0.57233 / 0.31 ( 9648) SS BOND : bond 0.01288 / 0.68 ( 2) SS BOND : angle 0.80172 / 0.50 ( 4) hydrogen bonds : bond 0.04935 / 3.18 ( 359) hydrogen bonds : angle 4.51951 / 3.14 ( 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 121 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.281 Fit side-chains REVERT: A 21 LYS cc_start: 0.8195 (ttpp) cc_final: 0.7979 (tttp) REVERT: A 264 SER cc_start: 0.8889 (p) cc_final: 0.8463 (m) REVERT: B 120 ILE cc_start: 0.9239 (mm) cc_final: 0.8981 (mm) REVERT: B 258 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.7832 (m-30) REVERT: R 162 MET cc_start: 0.6279 (mmt) cc_final: 0.5555 (mmt) REVERT: R 275 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.8017 (p90) outliers start: 14 outliers final: 9 residues processed: 118 average time/residue: 0.1050 time to fit residues: 15.9893 Evaluate side-chains 110 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 119 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: 1.9990 chunk 37 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.149673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.130971 restraints weight = 8672.825| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.43 r_work: 0.3382 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2690 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= 0.132 Angle : 0.532 6.530 9652 Z= 0.283 Chirality : 0.042 0.227 1117 Planarity : 0.004 0.045 1206 Dihedral : 4.307 17.264 948 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.98 % Allowed : 13.76 % 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: 0.64 (0.28), residues: 871 helix: 1.08 (0.26), residues: 425 sheet: 0.49 (0.38), residues: 174 loop : -0.53 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 291 TYR 0.014 0.001 TYR R 288 PHE 0.026 0.001 PHE R 275 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 7122) covalent geometry : angle 0.53196 / 0.28 ( 9648) SS BOND : bond 0.01020 / 0.54 ( 2) SS BOND : angle 0.61870 / 0.39 ( 4) hydrogen bonds : bond 0.04144 / 2.67 ( 359) hydrogen bonds : angle 4.31929 / 3.00 ( 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 129 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.267 Fit side-chains REVERT: A 241 MET cc_start: 0.3943 (ttm) cc_final: 0.3278 (tpt) REVERT: B 120 ILE cc_start: 0.9271 (mm) cc_final: 0.9015 (mm) REVERT: B 258 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.7818 (m-30) REVERT: G 40 TYR cc_start: 0.8617 (t80) cc_final: 0.8318 (t80) REVERT: R 162 MET cc_start: 0.6257 (mmt) cc_final: 0.5642 (mmt) REVERT: R 275 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7806 (p90) outliers start: 15 outliers final: 10 residues processed: 126 average time/residue: 0.1060 time to fit residues: 17.0677 Evaluate side-chains 117 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 84 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.149057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.131927 restraints weight = 8545.843| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.22 r_work: 0.3432 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2931 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= 0.117 Angle : 0.514 8.834 9652 Z= 0.271 Chirality : 0.042 0.234 1117 Planarity : 0.004 0.042 1206 Dihedral : 4.119 16.754 948 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.38 % Allowed : 13.76 % Favored : 83.86 % 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: 0.76 (0.29), residues: 871 helix: 1.29 (0.26), residues: 423 sheet: 0.36 (0.39), residues: 176 loop : -0.52 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 68 TYR 0.013 0.001 TYR R 288 PHE 0.023 0.001 PHE R 275 TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS R 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 7122) covalent geometry : angle 0.51427 / 0.27 ( 9648) SS BOND : bond 0.00912 / 0.48 ( 2) SS BOND : angle 0.54594 / 0.35 ( 4) hydrogen bonds : bond 0.03757 / 2.42 ( 359) hydrogen bonds : angle 4.16911 / 2.89 ( 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 127 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.280 Fit side-chains REVERT: A 241 MET cc_start: 0.3691 (ttm) cc_final: 0.3253 (tpt) REVERT: B 120 ILE cc_start: 0.9210 (mm) cc_final: 0.8923 (mm) REVERT: B 258 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7771 (m-30) REVERT: G 40 TYR cc_start: 0.8603 (t80) cc_final: 0.8386 (t80) REVERT: R 162 MET cc_start: 0.6162 (mmt) cc_final: 0.5499 (mmt) REVERT: R 275 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7653 (p90) outliers start: 18 outliers final: 12 residues processed: 123 average time/residue: 0.0993 time to fit residues: 15.9858 Evaluate side-chains 122 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 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 47 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 13 optimal weight: 0.2980 chunk 10 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 77 optimal weight: 0.0770 chunk 7 optimal weight: 0.7980 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.148968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.130604 restraints weight = 8475.502| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.36 r_work: 0.3432 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3075 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= 0.117 Angle : 0.515 7.949 9652 Z= 0.271 Chirality : 0.042 0.248 1117 Planarity : 0.004 0.043 1206 Dihedral : 4.017 16.975 948 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.51 % Allowed : 14.68 % Favored : 82.80 % 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: 0.84 (0.29), residues: 871 helix: 1.35 (0.26), residues: 423 sheet: 0.36 (0.39), residues: 176 loop : -0.45 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 68 TYR 0.009 0.001 TYR G 40 PHE 0.022 0.001 PHE R 275 TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS R 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 7122) covalent geometry : angle 0.51477 / 0.27 ( 9648) SS BOND : bond 0.00903 / 0.48 ( 2) SS BOND : angle 0.57141 / 0.37 ( 4) hydrogen bonds : bond 0.03611 / 2.33 ( 359) hydrogen bonds : angle 4.12473 / 2.85 ( 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 129 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.239 Fit side-chains REVERT: A 241 MET cc_start: 0.3646 (ttm) cc_final: 0.3285 (tpt) REVERT: A 244 MET cc_start: 0.8158 (tpp) cc_final: 0.7841 (tpp) REVERT: A 299 GLU cc_start: 0.8138 (tp30) cc_final: 0.7780 (tp30) REVERT: B 120 ILE cc_start: 0.9258 (mm) cc_final: 0.8985 (mm) REVERT: B 217 MET cc_start: 0.7041 (mmm) cc_final: 0.6838 (mmm) REVERT: B 258 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7809 (m-30) REVERT: G 40 TYR cc_start: 0.8599 (t80) cc_final: 0.8369 (t80) REVERT: R 162 MET cc_start: 0.6147 (mmt) cc_final: 0.5491 (mmt) REVERT: R 275 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7511 (p90) outliers start: 19 outliers final: 14 residues processed: 127 average time/residue: 0.0892 time to fit residues: 15.1163 Evaluate side-chains 117 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 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 119 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: 1.9990 chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 0.0670 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.147599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.129496 restraints weight = 8624.280| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.32 r_work: 0.3378 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7124 Z= 0.176 Angle : 0.565 9.239 9652 Z= 0.298 Chirality : 0.044 0.271 1117 Planarity : 0.004 0.045 1206 Dihedral : 4.152 17.652 948 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.04 % Allowed : 15.34 % 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 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: 0.72 (0.28), residues: 871 helix: 1.28 (0.26), residues: 421 sheet: 0.27 (0.38), residues: 179 loop : -0.53 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 68 TYR 0.009 0.001 TYR R 288 PHE 0.024 0.002 PHE R 275 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 ( 7122) covalent geometry : angle 0.56485 / 0.30 ( 9648) SS BOND : bond 0.01222 / 0.64 ( 2) SS BOND : angle 0.86756 / 0.55 ( 4) hydrogen bonds : bond 0.04146 / 2.69 ( 359) hydrogen bonds : angle 4.22811 / 2.93 ( 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 129 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.242 Fit side-chains REVERT: A 241 MET cc_start: 0.3762 (OUTLIER) cc_final: 0.3337 (tpt) REVERT: B 120 ILE cc_start: 0.9252 (mm) cc_final: 0.8969 (mm) REVERT: B 217 MET cc_start: 0.7116 (mmm) cc_final: 0.6914 (mmm) REVERT: B 234 PHE cc_start: 0.9196 (OUTLIER) cc_final: 0.8488 (m-80) REVERT: B 258 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.7915 (m-30) REVERT: G 40 TYR cc_start: 0.8650 (t80) cc_final: 0.8399 (t80) REVERT: R 162 MET cc_start: 0.6278 (mmt) cc_final: 0.5531 (mmt) REVERT: R 275 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7648 (p90) outliers start: 23 outliers final: 16 residues processed: 124 average time/residue: 0.0900 time to fit residues: 14.8180 Evaluate side-chains 124 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 241 MET 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 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 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 119 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: 0.9990 chunk 11 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 4 optimal weight: 0.0970 chunk 75 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.149324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.132155 restraints weight = 8574.490| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.23 r_work: 0.3433 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7124 Z= 0.112 Angle : 0.523 8.284 9652 Z= 0.274 Chirality : 0.042 0.262 1117 Planarity : 0.004 0.044 1206 Dihedral : 4.008 16.486 948 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.91 % Allowed : 14.95 % 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 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: 0.82 (0.28), residues: 871 helix: 1.41 (0.26), residues: 422 sheet: 0.24 (0.38), residues: 179 loop : -0.49 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 68 TYR 0.009 0.001 TYR R 288 PHE 0.020 0.001 PHE R 275 TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 7122) covalent geometry : angle 0.52307 / 0.27 ( 9648) SS BOND : bond 0.00793 / 0.42 ( 2) SS BOND : angle 0.53453 / 0.34 ( 4) hydrogen bonds : bond 0.03508 / 2.27 ( 359) hydrogen bonds : angle 4.12160 / 2.84 ( 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 134 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 241 MET cc_start: 0.3508 (ttm) cc_final: 0.3273 (tpt) REVERT: B 18 ILE cc_start: 0.8285 (mt) cc_final: 0.8022 (mt) REVERT: B 74 SER cc_start: 0.9249 (t) cc_final: 0.8965 (p) REVERT: B 120 ILE cc_start: 0.9188 (mm) cc_final: 0.8934 (mm) REVERT: B 234 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.8256 (m-80) REVERT: B 258 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7854 (m-30) REVERT: R 162 MET cc_start: 0.6292 (mmt) cc_final: 0.5561 (mmt) REVERT: R 275 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7444 (p90) outliers start: 22 outliers final: 15 residues processed: 130 average time/residue: 0.0883 time to fit residues: 15.4310 Evaluate side-chains 126 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 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 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 83 VAL Chi-restraints excluded: chain R residue 119 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: 1.9990 chunk 76 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 7 optimal weight: 0.0170 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.148571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.128980 restraints weight = 8649.449| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.50 r_work: 0.3398 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7124 Z= 0.121 Angle : 0.540 10.286 9652 Z= 0.282 Chirality : 0.042 0.270 1117 Planarity : 0.004 0.045 1206 Dihedral : 3.998 16.870 948 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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 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: 0.85 (0.29), residues: 871 helix: 1.43 (0.26), residues: 423 sheet: 0.19 (0.38), residues: 179 loop : -0.44 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 68 TYR 0.009 0.001 TYR R 288 PHE 0.020 0.001 PHE R 275 TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 7122) covalent geometry : angle 0.54000 / 0.28 ( 9648) SS BOND : bond 0.00899 / 0.47 ( 2) SS BOND : angle 0.61527 / 0.39 ( 4) hydrogen bonds : bond 0.03531 / 2.29 ( 359) hydrogen bonds : angle 4.09600 / 2.83 ( 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 132 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: B 18 ILE cc_start: 0.8076 (mt) cc_final: 0.7804 (mt) REVERT: B 74 SER cc_start: 0.9357 (t) cc_final: 0.9062 (p) REVERT: B 120 ILE cc_start: 0.9279 (mm) cc_final: 0.9008 (mm) REVERT: B 234 PHE cc_start: 0.9225 (OUTLIER) cc_final: 0.8432 (m-80) REVERT: B 258 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.7952 (m-30) REVERT: G 62 ARG cc_start: 0.7002 (mmp-170) cc_final: 0.6728 (mmt180) REVERT: R 162 MET cc_start: 0.6314 (mmt) cc_final: 0.5594 (mmt) REVERT: R 275 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7412 (p90) outliers start: 20 outliers final: 15 residues processed: 128 average time/residue: 0.0911 time to fit residues: 15.4805 Evaluate side-chains 127 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 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 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 83 VAL Chi-restraints excluded: chain R residue 119 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: 3.9990 chunk 33 optimal weight: 0.0070 chunk 34 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 54 optimal weight: 0.1980 chunk 21 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.151152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.134230 restraints weight = 8443.858| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.19 r_work: 0.3456 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7124 Z= 0.109 Angle : 0.540 10.552 9652 Z= 0.277 Chirality : 0.041 0.261 1117 Planarity : 0.004 0.042 1206 Dihedral : 3.926 16.457 948 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.25 % Allowed : 16.53 % Favored : 81.22 % 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: 0.98 (0.29), residues: 871 helix: 1.53 (0.26), residues: 424 sheet: 0.29 (0.37), residues: 179 loop : -0.40 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.017 0.001 TYR G 40 PHE 0.018 0.001 PHE R 275 TRP 0.015 0.001 TRP B 82 HIS 0.002 0.000 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 7122) covalent geometry : angle 0.53990 / 0.28 ( 9648) SS BOND : bond 0.00746 / 0.39 ( 2) SS BOND : angle 0.46016 / 0.29 ( 4) hydrogen bonds : bond 0.03254 / 2.11 ( 359) hydrogen bonds : angle 4.02422 / 2.78 ( 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 128 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 249 LYS cc_start: 0.7832 (mmmt) cc_final: 0.7531 (tppt) REVERT: B 18 ILE cc_start: 0.8244 (mt) cc_final: 0.7960 (mt) REVERT: B 74 SER cc_start: 0.9182 (t) cc_final: 0.8867 (p) REVERT: B 120 ILE cc_start: 0.9193 (mm) cc_final: 0.8895 (mm) REVERT: B 234 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8249 (m-80) REVERT: G 47 GLU cc_start: 0.8374 (mp0) cc_final: 0.8070 (mp0) REVERT: R 162 MET cc_start: 0.6284 (mmt) cc_final: 0.5548 (mmt) REVERT: R 275 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.7304 (p90) outliers start: 17 outliers final: 14 residues processed: 125 average time/residue: 0.0879 time to fit residues: 14.6257 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 : 0.197 ------------------------------------------------------------------------------- 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 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 161 SER Chi-restraints excluded: chain B residue 234 PHE 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 83 VAL Chi-restraints excluded: chain R residue 119 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: 6.9990 chunk 29 optimal weight: 0.0050 chunk 68 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 264 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.129885 restraints weight = 8543.032| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.39 r_work: 0.3424 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3474 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= 0.127 Angle : 0.549 10.346 9652 Z= 0.285 Chirality : 0.042 0.271 1117 Planarity : 0.004 0.043 1206 Dihedral : 3.968 16.910 948 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.51 % Allowed : 16.53 % Favored : 80.95 % 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: 0.98 (0.29), residues: 871 helix: 1.56 (0.26), residues: 422 sheet: 0.32 (0.38), residues: 174 loop : -0.44 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.008 0.001 TYR R 288 PHE 0.020 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/Z covalent geometry : bond 0.00293 / 0.13 ( 7122) covalent geometry : angle 0.54856 / 0.28 ( 9648) SS BOND : bond 0.00924 / 0.49 ( 2) SS BOND : angle 0.63197 / 0.40 ( 4) hydrogen bonds : bond 0.03479 / 2.26 ( 359) hydrogen bonds : angle 4.07083 / 2.82 ( 1050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1833.39 seconds wall clock time: 32 minutes 10.41 seconds (1930.41 seconds total)