Starting phenix.real_space_refine on Sun Sep 13 18:42:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rhx_24470/09_2026/7rhx_24470.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rhx_24470/09_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_24470/09_2026/7rhx_24470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rhx_24470/09_2026/7rhx_24470.map" model { file = "/net/cci-nas-00/data/ceres_data/7rhx_24470/09_2026/7rhx_24470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rhx_24470/09_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-2.2.1-6174/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: 4.59, 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: 2.47 Conformation dependent library (CDL) restraints added in 918.5 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: 3.95 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: 6.08 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: 44415 1.48 - 2.97: 2841 2.97 - 4.45: 201 4.45 - 5.94: 76 5.94 - 7.42: 11 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: 1.740 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: 0.120 Extract box with map and model: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.450 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.620 ------------------------------------------------------------------------------- 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 : 0.885 7.423 19904 Z= 0.707 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 0.88498 / 0.71 (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 : 0.654 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: 0.3259 time to fit residues: 70.4267 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 : 0.836 ------------------------------------------------------------------------------- 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: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 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... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.115052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.091372 restraints weight = 64391.837| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.14 r_work: 0.3115 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14208 Z= 0.188 Angle : 0.676 8.347 19904 Z= 0.418 Chirality : 0.043 0.348 2216 Planarity : 0.005 0.046 1984 Dihedral : 23.972 164.818 3320 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: 1.05 (0.23), residues: 1280 helix: 1.03 (0.18), residues: 792 sheet: -1.09 (0.63), residues: 64 loop : 0.62 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 187 TYR 0.012 0.001 TYR H 77 PHE 0.011 0.002 PHE B 265 TRP 0.013 0.002 TRP H 63 HIS 0.003 0.001 HIS H 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.19 (14208) covalent geometry : angle 0.67582 / 0.42 (19904) hydrogen bonds : bond 0.07332 / 4.84 ( 759) hydrogen bonds : angle 4.47785 / 3.27 ( 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 : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.8735 (mttt) cc_final: 0.8528 (ttpp) REVERT: G 49 CYS cc_start: 0.8768 (m) cc_final: 0.8500 (t) outliers start: 5 outliers final: 1 residues processed: 96 average time/residue: 0.2363 time to fit residues: 33.8133 Evaluate side-chains 83 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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: 4.9990 chunk 91 optimal weight: 3.9990 chunk 10 optimal weight: 0.0980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 323 ASN G 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.114260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.090344 restraints weight = 64652.022| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.15 r_work: 0.3100 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14208 Z= 0.182 Angle : 0.610 6.889 19904 Z= 0.384 Chirality : 0.041 0.343 2216 Planarity : 0.004 0.034 1984 Dihedral : 24.106 163.130 3320 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.47 % Allowed : 5.04 % Favored : 94.50 % 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: 1.29 (0.24), residues: 1280 helix: 1.41 (0.18), residues: 794 sheet: -1.62 (0.59), residues: 68 loop : 0.42 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 187 TYR 0.008 0.001 TYR H 77 PHE 0.009 0.001 PHE B 64 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 0.00326 / 0.18 (14208) covalent geometry : angle 0.61003 / 0.38 (19904) hydrogen bonds : bond 0.06836 / 4.55 ( 759) hydrogen bonds : angle 4.08337 / 3.00 ( 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: 5 poor density : 86 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 49 CYS cc_start: 0.8790 (m) cc_final: 0.8518 (t) outliers start: 5 outliers final: 2 residues processed: 87 average time/residue: 0.2234 time to fit residues: 29.5721 Evaluate side-chains 85 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER 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: 2.9990 chunk 50 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.111311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.087311 restraints weight = 64482.766| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.14 r_work: 0.3047 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14208 Z= 0.230 Angle : 0.649 6.907 19904 Z= 0.400 Chirality : 0.043 0.331 2216 Planarity : 0.004 0.035 1984 Dihedral : 24.302 163.155 3320 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.37 % Allowed : 6.53 % Favored : 93.10 % 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: 1.36 (0.18), residues: 790 sheet: -1.93 (0.57), residues: 68 loop : -0.08 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 297 TYR 0.012 0.001 TYR H 77 PHE 0.017 0.002 PHE B 64 TRP 0.012 0.002 TRP A 63 HIS 0.004 0.001 HIS H 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.23 (14208) covalent geometry : angle 0.64882 / 0.40 (19904) hydrogen bonds : bond 0.07748 / 5.11 ( 759) hydrogen bonds : angle 4.14664 / 3.04 ( 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 85 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.388 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 84 average time/residue: 0.2289 time to fit residues: 29.2075 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 : 0.427 ------------------------------------------------------------------------------- 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: 1.9990 chunk 32 optimal weight: 10.0000 chunk 54 optimal weight: 0.4980 chunk 58 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 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: 2.0988 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.112957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.089055 restraints weight = 64184.634| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.14 r_work: 0.3090 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2354 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= 0.160 Angle : 0.578 6.899 19904 Z= 0.366 Chirality : 0.039 0.319 2216 Planarity : 0.003 0.033 1984 Dihedral : 24.297 163.278 3320 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.47 % Allowed : 7.56 % Favored : 91.98 % 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: 1.23 (0.24), residues: 1280 helix: 1.56 (0.18), residues: 790 sheet: -1.95 (0.57), residues: 68 loop : 0.03 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 187 TYR 0.010 0.001 TYR H 77 PHE 0.010 0.001 PHE B 265 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 0.00279 / 0.16 (14208) covalent geometry : angle 0.57847 / 0.37 (19904) hydrogen bonds : bond 0.06317 / 4.19 ( 759) hydrogen bonds : angle 3.87630 / 2.85 ( 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 87 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.645 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 85 average time/residue: 0.2180 time to fit residues: 28.6558 Evaluate side-chains 85 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 15 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.113300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.089399 restraints weight = 64177.369| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.13 r_work: 0.3086 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14208 Z= 0.164 Angle : 0.565 6.432 19904 Z= 0.355 Chirality : 0.039 0.308 2216 Planarity : 0.003 0.032 1984 Dihedral : 24.325 163.005 3320 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.47 % Allowed : 7.84 % Favored : 91.70 % 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: 1.40 (0.24), residues: 1280 helix: 1.73 (0.18), residues: 790 sheet: -1.69 (0.58), residues: 64 loop : -0.07 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 106 TYR 0.006 0.001 TYR H 77 PHE 0.012 0.001 PHE B 64 TRP 0.010 0.001 TRP H 63 HIS 0.003 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 (14208) covalent geometry : angle 0.56461 / 0.36 (19904) hydrogen bonds : bond 0.05889 / 3.90 ( 759) hydrogen bonds : angle 3.75898 / 2.76 ( 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: 5 poor density : 85 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 89 average time/residue: 0.2021 time to fit residues: 28.0708 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 : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 287 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 138 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 125 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.111138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.087253 restraints weight = 64275.128| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.12 r_work: 0.3061 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2662 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= 0.208 Angle : 0.604 9.799 19904 Z= 0.375 Chirality : 0.041 0.315 2216 Planarity : 0.004 0.035 1984 Dihedral : 24.399 163.963 3320 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.65 % Allowed : 8.68 % 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: 1.17 (0.24), residues: 1280 helix: 1.63 (0.18), residues: 790 sheet: -2.08 (0.56), residues: 68 loop : -0.28 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 297 TYR 0.006 0.001 TYR A 77 PHE 0.011 0.001 PHE B 265 TRP 0.011 0.001 TRP G 52 HIS 0.004 0.001 HIS G 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.21 (14208) covalent geometry : angle 0.60394 / 0.37 (19904) hydrogen bonds : bond 0.07058 / 4.67 ( 759) hydrogen bonds : angle 3.92391 / 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 89 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.556 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 87 average time/residue: 0.2050 time to fit residues: 27.8964 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 : 0.645 ------------------------------------------------------------------------------- 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: 2.9990 chunk 125 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.112959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.089073 restraints weight = 64150.336| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.13 r_work: 0.3080 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14208 Z= 0.150 Angle : 0.558 6.617 19904 Z= 0.352 Chirality : 0.038 0.296 2216 Planarity : 0.003 0.033 1984 Dihedral : 24.367 163.577 3320 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.47 % Allowed : 8.68 % Favored : 90.86 % 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: 1.40 (0.24), residues: 1280 helix: 1.80 (0.18), residues: 792 sheet: -2.03 (0.57), residues: 68 loop : -0.15 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 154 TYR 0.006 0.001 TYR H 77 PHE 0.011 0.001 PHE B 64 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 0.00262 / 0.15 (14208) covalent geometry : angle 0.55800 / 0.35 (19904) hydrogen bonds : bond 0.05744 / 3.80 ( 759) hydrogen bonds : angle 3.70713 / 2.73 ( 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 87 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.667 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 86 average time/residue: 0.2045 time to fit residues: 27.5127 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 : 0.611 ------------------------------------------------------------------------------- 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: 7.9990 chunk 4 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.112067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.088082 restraints weight = 64408.147| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.14 r_work: 0.3062 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14208 Z= 0.183 Angle : 0.574 7.003 19904 Z= 0.358 Chirality : 0.039 0.300 2216 Planarity : 0.003 0.034 1984 Dihedral : 24.408 163.820 3320 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.47 % Allowed : 8.68 % Favored : 90.86 % 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: 1.32 (0.24), residues: 1280 helix: 1.78 (0.18), residues: 792 sheet: -2.08 (0.56), residues: 68 loop : -0.27 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 187 TYR 0.007 0.001 TYR H 77 PHE 0.010 0.001 PHE B 265 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 0.00353 / 0.18 (14208) covalent geometry : angle 0.57361 / 0.36 (19904) hydrogen bonds : bond 0.06280 / 4.16 ( 759) hydrogen bonds : angle 3.77845 / 2.78 ( 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: 5 poor density : 80 time to evaluate : 0.492 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 83 average time/residue: 0.2144 time to fit residues: 27.6378 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 : 0.616 ------------------------------------------------------------------------------- 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 28 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.111056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.087137 restraints weight = 64345.558| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.13 r_work: 0.3060 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2913 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= 0.199 Angle : 0.590 6.717 19904 Z= 0.367 Chirality : 0.040 0.299 2216 Planarity : 0.004 0.035 1984 Dihedral : 24.473 164.544 3320 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.37 % Allowed : 8.77 % Favored : 90.86 % 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: 1.17 (0.24), residues: 1280 helix: 1.70 (0.18), residues: 792 sheet: -2.04 (0.57), residues: 68 loop : -0.44 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 297 TYR 0.008 0.001 TYR H 77 PHE 0.013 0.001 PHE B 64 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 0.00391 / 0.20 (14208) covalent geometry : angle 0.58992 / 0.37 (19904) hydrogen bonds : bond 0.06834 / 4.51 ( 759) hydrogen bonds : angle 3.86500 / 2.84 ( 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 84 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.639 Fit side-chains REVERT: G 28 MET cc_start: 0.8886 (mmp) cc_final: 0.8668 (mmp) outliers start: 4 outliers final: 4 residues processed: 83 average time/residue: 0.2050 time to fit residues: 26.3516 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 : 0.541 ------------------------------------------------------------------------------- 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 121 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 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: 9.9990 chunk 90 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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 = 0.111250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.087398 restraints weight = 64075.016| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.12 r_work: 0.3065 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14208 Z= 0.188 Angle : 0.581 7.452 19904 Z= 0.362 Chirality : 0.039 0.296 2216 Planarity : 0.004 0.034 1984 Dihedral : 24.500 164.120 3320 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.47 % Allowed : 8.68 % Favored : 90.86 % 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: 1.18 (0.24), residues: 1280 helix: 1.72 (0.18), residues: 792 sheet: -2.05 (0.57), residues: 68 loop : -0.47 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 187 TYR 0.008 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 G 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.19 (14208) covalent geometry : angle 0.58104 / 0.36 (19904) hydrogen bonds : bond 0.06551 / 4.33 ( 759) hydrogen bonds : angle 3.83143 / 2.82 ( 2036) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5694.52 seconds wall clock time: 96 minutes 51.20 seconds (5811.20 seconds total)