Starting phenix.real_space_refine on Sun Jul 5 03:03:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rhx_24470/07_2026/7rhx_24470.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rhx_24470/07_2026/7rhx_24470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rhx_24470/07_2026/7rhx_24470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rhx_24470/07_2026/7rhx_24470.map" model { file = "/net/cci-nas-00/data/ceres_data/7rhx_24470/07_2026/7rhx_24470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rhx_24470/07_2026/7rhx_24470.cif" } resolution = 3.23 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= 0.081 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: 6 Type Number sf(0) Gaussians P 168 5.49 5 S 60 5.16 5 C 7970 2.51 5 N 2562 2.21 5 O 2868 1.98 5 H 12159 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25787 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 5110 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 7, 'TRANS': 314} Chain: "B" Number of atoms: 5111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 5111 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 7, 'TRANS': 314} Chain: "C" Number of atoms: 1329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 1329 Classifications: {'DNA': 42} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 41} Chain: "D" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 1344 Classifications: {'DNA': 42} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 41} Chain: "E" Number of atoms: 1329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 1329 Classifications: {'DNA': 42} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 41} Chain: "F" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 1344 Classifications: {'DNA': 42} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 41} Chain: "G" Number of atoms: 5110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 5110 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 7, 'TRANS': 314} Chain: "H" Number of atoms: 5110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 5110 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 7, 'TRANS': 314} Time building chain proxies: 4.57, per 1000 atoms: 0.18 Number of scatterers: 25787 At special positions: 0 Unit cell: (87.203, 164.517, 180.699, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 168 15.00 O 2868 8.00 N 2562 7.00 C 7970 6.00 H 12159 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 615.5 milliseconds 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 5 sheets defined 68.8% alpha, 2.3% beta 84 base pairs and 147 stacking pairs defined. Time for finding SS restraints: 4.41 Creating SS restraints... Processing helix chain 'A' and resid 20 through 32 removed outlier: 3.633A pdb=" N ARG A 24 " --> pdb=" O SER A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 37 Processing helix chain 'A' and resid 38 through 59 removed outlier: 3.696A pdb=" N MET A 44 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 47 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 82 removed outlier: 3.883A pdb=" N ASP A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 103 Processing helix chain 'A' and resid 106 through 109 Processing helix chain 'A' and resid 110 through 127 removed outlier: 3.672A pdb=" N SER A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'A' and resid 154 through 171 Processing helix chain 'A' and resid 173 through 178 Processing helix chain 'A' and resid 179 through 180 No H-bonds generated for 'chain 'A' and resid 179 through 180' Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 214 through 229 removed outlier: 3.782A pdb=" N LEU A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 233 removed outlier: 3.981A pdb=" N ASP A 233 " --> pdb=" O VAL A 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 230 through 233' Processing helix chain 'A' and resid 257 through 273 removed outlier: 3.519A pdb=" N GLY A 263 " --> pdb=" O ARG A 259 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 302 Processing helix chain 'A' and resid 305 through 314 removed outlier: 3.566A pdb=" N ALA A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 326 removed outlier: 4.422A pdb=" N VAL A 321 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 325 " --> pdb=" O VAL A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 341 removed outlier: 4.459A pdb=" N VAL A 336 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 33 Processing helix chain 'B' and resid 34 through 37 Processing helix chain 'B' and resid 38 through 59 removed outlier: 3.501A pdb=" N TRP B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 81 removed outlier: 3.645A pdb=" N ARG B 81 " --> pdb=" O TYR B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 103 removed outlier: 3.839A pdb=" N LEU B 95 " --> pdb=" O HIS B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 109 Processing helix chain 'B' and resid 110 through 127 removed outlier: 3.777A pdb=" N VAL B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 154 through 171 Processing helix chain 'B' and resid 173 through 178 Processing helix chain 'B' and resid 179 through 180 No H-bonds generated for 'chain 'B' and resid 179 through 180' Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 214 through 229 Processing helix chain 'B' and resid 230 through 233 removed outlier: 3.726A pdb=" N ASP B 233 " --> pdb=" O VAL B 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 230 through 233' Processing helix chain 'B' and resid 257 through 274 removed outlier: 3.580A pdb=" N PHE B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 303 Processing helix chain 'B' and resid 305 through 314 Processing helix chain 'B' and resid 318 through 325 removed outlier: 3.708A pdb=" N MET B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 332 Processing helix chain 'B' and resid 333 through 340 Processing helix chain 'G' and resid 21 through 33 Processing helix chain 'G' and resid 34 through 37 Processing helix chain 'G' and resid 38 through 59 removed outlier: 3.599A pdb=" N MET G 44 " --> pdb=" O HIS G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 81 removed outlier: 3.550A pdb=" N ARG G 81 " --> pdb=" O TYR G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 103 removed outlier: 3.553A pdb=" N LEU G 95 " --> pdb=" O HIS G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 109 Processing helix chain 'G' and resid 110 through 127 removed outlier: 3.772A pdb=" N SER G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 150 Processing helix chain 'G' and resid 154 through 171 removed outlier: 3.513A pdb=" N ASN G 160 " --> pdb=" O GLN G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 179 removed outlier: 3.513A pdb=" N ARG G 179 " --> pdb=" O ALA G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 183 No H-bonds generated for 'chain 'G' and resid 181 through 183' Processing helix chain 'G' and resid 214 through 228 removed outlier: 3.538A pdb=" N ARG G 223 " --> pdb=" O LYS G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 233 removed outlier: 3.585A pdb=" N ASP G 233 " --> pdb=" O VAL G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 274 removed outlier: 3.657A pdb=" N ILE G 264 " --> pdb=" O ALA G 260 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE G 265 " --> pdb=" O LEU G 261 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE G 272 " --> pdb=" O THR G 268 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 302 removed outlier: 3.556A pdb=" N ALA G 302 " --> pdb=" O ASP G 298 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 314 Processing helix chain 'G' and resid 317 through 326 removed outlier: 4.380A pdb=" N VAL G 321 " --> pdb=" O ASN G 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 332 Processing helix chain 'G' and resid 333 through 340 removed outlier: 3.540A pdb=" N ARG G 337 " --> pdb=" O GLY G 333 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 33 Processing helix chain 'H' and resid 34 through 37 Processing helix chain 'H' and resid 38 through 59 removed outlier: 3.703A pdb=" N TRP H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS H 43 " --> pdb=" O GLU H 39 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET H 44 " --> pdb=" O HIS H 40 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU H 45 " --> pdb=" O THR H 41 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER H 51 " --> pdb=" O SER H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 82 removed outlier: 3.653A pdb=" N ASP H 73 " --> pdb=" O GLU H 69 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY H 82 " --> pdb=" O LEU H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 103 removed outlier: 3.728A pdb=" N LEU H 95 " --> pdb=" O HIS H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 109 removed outlier: 3.605A pdb=" N ASP H 109 " --> pdb=" O ARG H 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 106 through 109' Processing helix chain 'H' and resid 110 through 127 removed outlier: 3.628A pdb=" N ARG H 118 " --> pdb=" O SER H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 150 Processing helix chain 'H' and resid 154 through 171 Processing helix chain 'H' and resid 173 through 178 Processing helix chain 'H' and resid 179 through 180 No H-bonds generated for 'chain 'H' and resid 179 through 180' Processing helix chain 'H' and resid 181 through 183 No H-bonds generated for 'chain 'H' and resid 181 through 183' Processing helix chain 'H' and resid 216 through 229 removed outlier: 4.068A pdb=" N LEU H 220 " --> pdb=" O GLY H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 233 removed outlier: 3.863A pdb=" N ASP H 233 " --> pdb=" O VAL H 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 230 through 233' Processing helix chain 'H' and resid 257 through 274 removed outlier: 3.936A pdb=" N GLY H 263 " --> pdb=" O ARG H 259 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE H 264 " --> pdb=" O ALA H 260 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE H 265 " --> pdb=" O LEU H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 289 through 302 Processing helix chain 'H' and resid 305 through 314 Processing helix chain 'H' and resid 318 through 325 removed outlier: 4.121A pdb=" N MET H 322 " --> pdb=" O VAL H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 328 No H-bonds generated for 'chain 'H' and resid 326 through 328' Processing helix chain 'H' and resid 329 through 332 Processing helix chain 'H' and resid 333 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 187 Processing sheet with id=AA2, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AA3, first strand: chain 'G' and resid 185 through 187 Processing sheet with id=AA4, first strand: chain 'H' and resid 185 through 187 Processing sheet with id=AA5, first strand: chain 'H' and resid 241 through 242 removed outlier: 4.512A pdb=" N ARG H 241 " --> pdb=" O ALA H 249 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1632 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 202 hydrogen bonds 404 hydrogen bond angles 0 basepair planarities 84 basepair parallelities 147 stacking parallelities Total time for adding SS restraints: 5.81 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12143 1.03 - 1.23: 102 1.23 - 1.42: 6083 1.42 - 1.61: 7933 1.61 - 1.81: 106 Bond restraints: 26367 Sorted by residual: bond pdb=" C3' DC C 15 " pdb=" C2' DC C 15 " ideal model delta sigma weight residual 1.516 1.554 -0.038 8.00e-03 1.56e+04 2.23e+01 bond pdb=" C3' DA E 33 " pdb=" C2' DA E 33 " ideal model delta sigma weight residual 1.516 1.550 -0.034 8.00e-03 1.56e+04 1.81e+01 bond pdb=" C3' DC E 8 " pdb=" C2' DC E 8 " ideal model delta sigma weight residual 1.516 1.549 -0.033 8.00e-03 1.56e+04 1.72e+01 bond pdb=" C3' DA E 11 " pdb=" C2' DA E 11 " ideal model delta sigma weight residual 1.516 1.549 -0.033 8.00e-03 1.56e+04 1.69e+01 bond pdb=" C3' DT D 31 " pdb=" C2' DT D 31 " ideal model delta sigma weight residual 1.516 1.549 -0.033 8.00e-03 1.56e+04 1.68e+01 ... (remaining 26362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 44459 1.48 - 2.97: 2803 2.97 - 4.45: 196 4.45 - 5.94: 76 5.94 - 7.42: 10 Bond angle restraints: 47544 Sorted by residual: angle pdb=" O4' DC C 19 " pdb=" C1' DC C 19 " pdb=" N1 DC C 19 " ideal model delta sigma weight residual 108.00 113.11 -5.11 7.00e-01 2.04e+00 5.33e+01 angle pdb=" O4' DG D 27 " pdb=" C1' DG D 27 " pdb=" N9 DG D 27 " ideal model delta sigma weight residual 108.00 112.54 -4.54 7.00e-01 2.04e+00 4.20e+01 angle pdb=" C4' DC F 21 " pdb=" O4' DC F 21 " pdb=" C1' DC F 21 " ideal model delta sigma weight residual 110.10 103.66 6.44 1.00e+00 1.00e+00 4.14e+01 angle pdb=" O5' DT C 31 " pdb=" C5' DT C 31 " pdb=" C4' DT C 31 " ideal model delta sigma weight residual 109.40 114.22 -4.82 8.00e-01 1.56e+00 3.63e+01 angle pdb=" O5' DT C 21 " pdb=" C5' DT C 21 " pdb=" C4' DT C 21 " ideal model delta sigma weight residual 109.40 114.16 -4.76 8.00e-01 1.56e+00 3.54e+01 ... (remaining 47539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.87: 10707 34.87 - 69.73: 954 69.73 - 104.60: 12 104.60 - 139.47: 0 139.47 - 174.33: 4 Dihedral angle restraints: 11677 sinusoidal: 7444 harmonic: 4233 Sorted by residual: dihedral pdb=" CA THR B 206 " pdb=" C THR B 206 " pdb=" N ALA B 207 " pdb=" CA ALA B 207 " ideal model delta harmonic sigma weight residual 180.00 152.39 27.61 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA LYS A 62 " pdb=" C LYS A 62 " pdb=" N TRP A 63 " pdb=" CA TRP A 63 " ideal model delta harmonic sigma weight residual -180.00 -158.14 -21.86 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA LYS B 62 " pdb=" C LYS B 62 " pdb=" N TRP B 63 " pdb=" CA TRP B 63 " ideal model delta harmonic sigma weight residual 180.00 -159.46 -20.54 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 11674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1864 0.071 - 0.142: 281 0.142 - 0.212: 64 0.212 - 0.283: 4 0.283 - 0.354: 3 Chirality restraints: 2216 Sorted by residual: chirality pdb=" C3' DC E 15 " pdb=" C4' DC E 15 " pdb=" O3' DC E 15 " pdb=" C2' DC E 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" C3' DT E 34 " pdb=" C4' DT E 34 " pdb=" O3' DT E 34 " pdb=" C2' DT E 34 " both_signs ideal model delta sigma weight residual False -2.73 -2.40 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" C3' DG C 14 " pdb=" C4' DG C 14 " pdb=" O3' DG C 14 " pdb=" C2' DG C 14 " both_signs ideal model delta sigma weight residual False -2.73 -2.45 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 2213 not shown) Planarity restraints: 3358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 124 " 0.035 2.00e-02 2.50e+03 4.27e-02 2.74e+01 pdb=" CG ASN G 124 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN G 124 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN G 124 " -0.067 2.00e-02 2.50e+03 pdb="HD21 ASN G 124 " -0.001 2.00e-02 2.50e+03 pdb="HD22 ASN G 124 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG E 36 " -0.053 2.00e-02 2.50e+03 2.35e-02 1.93e+01 pdb=" N9 DG E 36 " 0.068 2.00e-02 2.50e+03 pdb=" C8 DG E 36 " -0.008 2.00e-02 2.50e+03 pdb=" N7 DG E 36 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DG E 36 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG E 36 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG E 36 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DG E 36 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG E 36 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG E 36 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG E 36 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG E 36 " 0.005 2.00e-02 2.50e+03 pdb=" H8 DG E 36 " 0.002 2.00e-02 2.50e+03 pdb=" H1 DG E 36 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT C 31 " 0.052 2.00e-02 2.50e+03 2.50e-02 1.87e+01 pdb=" N1 DT C 31 " -0.067 2.00e-02 2.50e+03 pdb=" C2 DT C 31 " 0.011 2.00e-02 2.50e+03 pdb=" O2 DT C 31 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DT C 31 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT C 31 " 0.005 2.00e-02 2.50e+03 pdb=" O4 DT C 31 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DT C 31 " 0.003 2.00e-02 2.50e+03 pdb=" C7 DT C 31 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DT C 31 " -0.007 2.00e-02 2.50e+03 pdb=" H3 DT C 31 " 0.002 2.00e-02 2.50e+03 pdb=" H6 DT C 31 " -0.006 2.00e-02 2.50e+03 ... (remaining 3355 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 789 2.17 - 2.78: 44887 2.78 - 3.39: 63554 3.39 - 3.99: 82968 3.99 - 4.60: 132221 Nonbonded interactions: 324419 Sorted by model distance: nonbonded pdb=" HG SER B 257 " pdb=" OP2 DT C 6 " model vdw 1.567 2.450 nonbonded pdb=" HG SER B 205 " pdb=" O ALA B 207 " model vdw 1.596 2.450 nonbonded pdb=" O LEU B 215 " pdb=" HG1 THR B 218 " model vdw 1.614 2.450 nonbonded pdb=" HG SER A 287 " pdb=" OP1 DA C 25 " model vdw 1.627 2.450 nonbonded pdb="HH12 ARG G 187 " pdb=" OE2 GLU G 222 " model vdw 1.641 2.450 ... (remaining 324414 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 20 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 341)) selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 1.040 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: 0.110 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 27.770 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14208 Z= 0.474 Angle : 0.878 7.423 19904 Z= 0.699 Chirality : 0.056 0.354 2216 Planarity : 0.012 0.110 1984 Dihedral : 20.665 174.333 5768 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: -0.38 (0.22), residues: 1280 helix: -0.34 (0.17), residues: 772 sheet: -0.99 (0.62), residues: 68 loop : 0.44 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG B 292 TYR 0.016 0.004 TYR G 237 PHE 0.021 0.002 PHE A 31 TRP 0.018 0.004 TRP H 315 HIS 0.007 0.002 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.47 (14208) covalent geometry : angle 0.87800 / 0.70 (19904) hydrogen bonds : bond 0.15415 / 10.70 ( 759) hydrogen bonds : angle 5.64424 / 4.17 ( 2036) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.8335 (tpt) cc_final: 0.8119 (tpt) REVERT: G 25 LYS cc_start: 0.8920 (mttt) cc_final: 0.8710 (ttpp) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.3862 time to fit residues: 82.2191 Evaluate side-chains 91 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.114955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.091279 restraints weight = 64382.114| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.15 r_work: 0.3114 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14208 Z= 0.183 Angle : 0.674 8.416 19904 Z= 0.419 Chirality : 0.044 0.320 2216 Planarity : 0.005 0.046 1984 Dihedral : 23.990 165.759 3320 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.47 % Allowed : 4.29 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.06 (0.23), residues: 1280 helix: 1.03 (0.18), residues: 790 sheet: -1.08 (0.63), residues: 64 loop : 0.65 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 326 TYR 0.012 0.001 TYR H 77 PHE 0.011 0.002 PHE B 265 TRP 0.013 0.002 TRP A 63 HIS 0.003 0.001 HIS A 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.18 (14208) covalent geometry : angle 0.67354 / 0.42 (19904) hydrogen bonds : bond 0.07382 / 4.88 ( 759) hydrogen bonds : angle 4.50029 / 3.29 ( 2036) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: G 25 LYS cc_start: 0.8732 (mttt) cc_final: 0.8523 (ttpp) REVERT: G 49 CYS cc_start: 0.8773 (m) cc_final: 0.8499 (t) outliers start: 5 outliers final: 1 residues processed: 96 average time/residue: 0.2531 time to fit residues: 36.3129 Evaluate side-chains 81 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 200 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 29 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 323 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.115371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.091583 restraints weight = 64680.272| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.15 r_work: 0.3121 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14208 Z= 0.162 Angle : 0.592 6.954 19904 Z= 0.376 Chirality : 0.040 0.312 2216 Planarity : 0.004 0.071 1984 Dihedral : 24.108 164.056 3320 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.37 % Allowed : 5.04 % Favored : 94.59 % 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: 1.42 (0.24), residues: 1280 helix: 1.48 (0.18), residues: 794 sheet: -1.54 (0.59), residues: 68 loop : 0.53 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 106 TYR 0.008 0.001 TYR H 77 PHE 0.008 0.001 PHE B 265 TRP 0.010 0.001 TRP H 63 HIS 0.004 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.16 (14208) covalent geometry : angle 0.59157 / 0.38 (19904) hydrogen bonds : bond 0.06303 / 4.19 ( 759) hydrogen bonds : angle 4.00638 / 2.94 ( 2036) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: G 49 CYS cc_start: 0.8781 (m) cc_final: 0.8518 (t) outliers start: 4 outliers final: 1 residues processed: 88 average time/residue: 0.2455 time to fit residues: 32.5592 Evaluate side-chains 85 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 200 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 2 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 323 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.110923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.086941 restraints weight = 64555.732| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.15 r_work: 0.3037 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14208 Z= 0.260 Angle : 0.663 7.254 19904 Z= 0.409 Chirality : 0.044 0.319 2216 Planarity : 0.004 0.035 1984 Dihedral : 24.314 165.177 3320 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.37 % Allowed : 6.44 % Favored : 93.19 % 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: 0.99 (0.23), residues: 1280 helix: 1.34 (0.18), residues: 788 sheet: -1.92 (0.57), residues: 68 loop : -0.03 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 106 TYR 0.011 0.001 TYR H 77 PHE 0.016 0.002 PHE B 64 TRP 0.012 0.002 TRP A 63 HIS 0.005 0.002 HIS H 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.26 (14208) covalent geometry : angle 0.66308 / 0.41 (19904) hydrogen bonds : bond 0.08246 / 5.45 ( 759) hydrogen bonds : angle 4.22444 / 3.10 ( 2036) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.672 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 83 average time/residue: 0.2337 time to fit residues: 30.2422 Evaluate side-chains 81 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain H residue 200 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 73 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.112286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.088364 restraints weight = 64219.204| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.14 r_work: 0.3075 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14208 Z= 0.177 Angle : 0.593 6.903 19904 Z= 0.374 Chirality : 0.040 0.299 2216 Planarity : 0.004 0.033 1984 Dihedral : 24.326 164.719 3320 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.47 % Allowed : 7.28 % Favored : 92.26 % 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: 1.14 (0.24), residues: 1280 helix: 1.48 (0.18), residues: 790 sheet: -2.00 (0.57), residues: 68 loop : -0.01 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 187 TYR 0.011 0.001 TYR H 77 PHE 0.012 0.001 PHE B 64 TRP 0.012 0.001 TRP G 52 HIS 0.003 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.18 (14208) covalent geometry : angle 0.59278 / 0.37 (19904) hydrogen bonds : bond 0.06785 / 4.49 ( 759) hydrogen bonds : angle 3.96221 / 2.90 ( 2036) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.717 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 87 average time/residue: 0.2309 time to fit residues: 31.1963 Evaluate side-chains 85 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 289 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 94 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.112385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.088439 restraints weight = 64246.356| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.14 r_work: 0.3068 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14208 Z= 0.178 Angle : 0.577 6.590 19904 Z= 0.364 Chirality : 0.039 0.293 2216 Planarity : 0.003 0.033 1984 Dihedral : 24.356 164.212 3320 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.56 % Allowed : 8.02 % Favored : 91.42 % 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: 1.25 (0.24), residues: 1280 helix: 1.61 (0.18), residues: 790 sheet: -1.78 (0.58), residues: 64 loop : -0.12 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 297 TYR 0.009 0.001 TYR H 77 PHE 0.011 0.001 PHE B 64 TRP 0.010 0.001 TRP G 52 HIS 0.004 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.18 (14208) covalent geometry : angle 0.57687 / 0.36 (19904) hydrogen bonds : bond 0.06328 / 4.19 ( 759) hydrogen bonds : angle 3.85864 / 2.83 ( 2036) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.680 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 87 average time/residue: 0.2362 time to fit residues: 32.3104 Evaluate side-chains 89 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain H residue 289 HIS Chi-restraints excluded: chain H residue 299 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 138 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.111313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.087356 restraints weight = 64277.379| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.14 r_work: 0.3048 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14208 Z= 0.202 Angle : 0.594 6.742 19904 Z= 0.372 Chirality : 0.040 0.293 2216 Planarity : 0.004 0.034 1984 Dihedral : 24.417 165.008 3320 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.65 % Allowed : 8.21 % Favored : 91.14 % 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: 1.15 (0.24), residues: 1280 helix: 1.59 (0.18), residues: 790 sheet: -1.82 (0.57), residues: 64 loop : -0.29 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 297 TYR 0.007 0.001 TYR H 77 PHE 0.012 0.001 PHE B 64 TRP 0.011 0.001 TRP G 52 HIS 0.004 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.20 (14208) covalent geometry : angle 0.59393 / 0.37 (19904) hydrogen bonds : bond 0.06888 / 4.55 ( 759) hydrogen bonds : angle 3.92657 / 2.88 ( 2036) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.636 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 89 average time/residue: 0.2222 time to fit residues: 30.5710 Evaluate side-chains 86 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain H residue 289 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 18 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.112358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.088474 restraints weight = 64187.050| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.13 r_work: 0.3079 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14208 Z= 0.163 Angle : 0.567 6.656 19904 Z= 0.357 Chirality : 0.039 0.280 2216 Planarity : 0.003 0.033 1984 Dihedral : 24.399 164.298 3320 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.37 % Allowed : 8.68 % Favored : 90.95 % 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: 1.30 (0.24), residues: 1280 helix: 1.71 (0.18), residues: 792 sheet: -2.04 (0.57), residues: 68 loop : -0.18 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 297 TYR 0.006 0.001 TYR H 77 PHE 0.011 0.001 PHE B 265 TRP 0.011 0.001 TRP G 52 HIS 0.003 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.16 (14208) covalent geometry : angle 0.56713 / 0.36 (19904) hydrogen bonds : bond 0.06049 / 4.00 ( 759) hydrogen bonds : angle 3.77318 / 2.77 ( 2036) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.647 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 85 average time/residue: 0.2198 time to fit residues: 28.8484 Evaluate side-chains 84 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain H residue 289 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 49 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 10 optimal weight: 0.3980 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.112258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.088397 restraints weight = 64481.838| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.13 r_work: 0.3083 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14208 Z= 0.168 Angle : 0.563 7.698 19904 Z= 0.354 Chirality : 0.038 0.279 2216 Planarity : 0.003 0.034 1984 Dihedral : 24.424 164.713 3320 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.37 % Allowed : 8.86 % Favored : 90.76 % 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: 1.33 (0.24), residues: 1280 helix: 1.78 (0.18), residues: 792 sheet: -2.03 (0.57), residues: 68 loop : -0.24 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 297 TYR 0.007 0.001 TYR B 324 PHE 0.010 0.001 PHE B 64 TRP 0.010 0.001 TRP G 52 HIS 0.003 0.001 HIS G 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.17 (14208) covalent geometry : angle 0.56313 / 0.35 (19904) hydrogen bonds : bond 0.06032 / 4.00 ( 759) hydrogen bonds : angle 3.74943 / 2.76 ( 2036) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.760 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 84 average time/residue: 0.2332 time to fit residues: 30.1252 Evaluate side-chains 84 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain H residue 289 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 28 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 112 optimal weight: 0.0000 chunk 78 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.112118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.088237 restraints weight = 64356.682| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.13 r_work: 0.3078 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14208 Z= 0.170 Angle : 0.567 10.367 19904 Z= 0.354 Chirality : 0.038 0.274 2216 Planarity : 0.003 0.033 1984 Dihedral : 24.442 165.080 3320 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.47 % Allowed : 8.86 % Favored : 90.67 % 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: 1.33 (0.24), residues: 1280 helix: 1.79 (0.18), residues: 792 sheet: -2.04 (0.57), residues: 68 loop : -0.28 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 297 TYR 0.007 0.001 TYR H 77 PHE 0.011 0.001 PHE B 64 TRP 0.010 0.001 TRP G 52 HIS 0.003 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.17 (14208) covalent geometry : angle 0.56718 / 0.35 (19904) hydrogen bonds : bond 0.06051 / 4.00 ( 759) hydrogen bonds : angle 3.74277 / 2.75 ( 2036) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.779 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 83 average time/residue: 0.2020 time to fit residues: 26.4071 Evaluate side-chains 84 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain H residue 289 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.110871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.086948 restraints weight = 64152.938| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.14 r_work: 0.3043 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 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 : 0.004 0.027 14208 Z= 0.207 Angle : 0.591 7.387 19904 Z= 0.367 Chirality : 0.040 0.280 2216 Planarity : 0.004 0.035 1984 Dihedral : 24.503 165.676 3320 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.47 % Allowed : 8.77 % Favored : 90.76 % 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: 1.14 (0.24), residues: 1280 helix: 1.68 (0.18), residues: 792 sheet: -2.09 (0.56), residues: 68 loop : -0.45 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 187 TYR 0.008 0.001 TYR H 77 PHE 0.012 0.001 PHE B 64 TRP 0.010 0.001 TRP G 52 HIS 0.004 0.001 HIS G 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.21 (14208) covalent geometry : angle 0.59138 / 0.37 (19904) hydrogen bonds : bond 0.06872 / 4.54 ( 759) hydrogen bonds : angle 3.87076 / 2.84 ( 2036) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5999.02 seconds wall clock time: 102 minutes 15.52 seconds (6135.52 seconds total)