Starting phenix.real_space_refine on Tue Apr 7 05:02:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rhx_24470/04_2026/7rhx_24470.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rhx_24470/04_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_24470/04_2026/7rhx_24470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rhx_24470/04_2026/7rhx_24470.map" model { file = "/net/cci-nas-00/data/ceres_data/7rhx_24470/04_2026/7rhx_24470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rhx_24470/04_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-2.1rc1-6017/lib/python3.9/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: 4.44, per 1000 atoms: 0.17 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: 2.05 Conformation dependent library (CDL) restraints added in 817.5 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: 4.31 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: 5.65 Time building geometry restraints manager: 2.96 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=" N SER G 20 " pdb=" CA SER G 20 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N SER H 20 " pdb=" CA SER H 20 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.90e+00 bond pdb=" N SER B 20 " pdb=" CA SER B 20 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.90e+00 bond pdb=" N SER A 20 " pdb=" CA SER A 20 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" C4' DC C 15 " pdb=" O4' DC C 15 " ideal model delta sigma weight residual 1.450 1.419 0.031 2.00e-02 2.50e+03 2.35e+00 ... (remaining 26362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 44461 1.45 - 2.91: 2891 2.91 - 4.36: 162 4.36 - 5.81: 24 5.81 - 7.27: 6 Bond angle restraints: 47544 Sorted by residual: angle pdb=" C3' DT E 34 " pdb=" O3' DT E 34 " pdb=" P DC E 35 " ideal model delta sigma weight residual 120.20 126.34 -6.14 1.50e+00 4.44e-01 1.67e+01 angle pdb=" C4' DC F 21 " pdb=" O4' DC F 21 " pdb=" C1' DC F 21 " ideal model delta sigma weight residual 109.70 103.66 6.04 1.50e+00 4.44e-01 1.62e+01 angle pdb=" C3' DG E 14 " pdb=" O3' DG E 14 " pdb=" P DC E 15 " ideal model delta sigma weight residual 120.20 125.74 -5.54 1.50e+00 4.44e-01 1.37e+01 angle pdb=" O3' DG C 14 " pdb=" C3' DG C 14 " pdb=" C2' DG C 14 " ideal model delta sigma weight residual 111.50 116.82 -5.32 1.50e+00 4.44e-01 1.26e+01 angle pdb=" O3' DC E 15 " pdb=" C3' DC E 15 " pdb=" C2' DC E 15 " ideal model delta sigma weight residual 111.50 116.80 -5.30 1.50e+00 4.44e-01 1.25e+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 - 0.057: 1810 0.057 - 0.113: 351 0.113 - 0.170: 48 0.170 - 0.227: 5 0.227 - 0.284: 2 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 -2.66 -2.38 -0.28 2.00e-01 2.50e+01 2.01e+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 -2.66 -2.40 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C1' DT C 31 " pdb=" O4' DT C 31 " pdb=" C2' DT C 31 " pdb=" N1 DT C 31 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.25e+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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 26.470 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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 : 0.004 0.039 14208 Z= 0.211 Angle : 0.790 7.267 19904 Z= 0.509 Chirality : 0.046 0.284 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 covalent geometry : bond 0.00437 (14208) covalent geometry : angle 0.78966 (19904) hydrogen bonds : bond 0.15415 ( 759) hydrogen bonds : angle 5.64424 ( 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 : 0.584 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: 0.3621 time to fit residues: 76.1514 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 : 0.592 ------------------------------------------------------------------------------- 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: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 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... Flipped N/Q/H residues before XYZ refinement: B 323 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.115037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.091301 restraints weight = 64439.694| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.15 r_work: 0.3116 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14208 Z= 0.182 Angle : 0.619 6.572 19904 Z= 0.374 Chirality : 0.038 0.141 2216 Planarity : 0.004 0.037 1984 Dihedral : 23.922 164.492 3320 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.47 % Allowed : 3.92 % Favored : 95.62 % 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: 1.13 (0.23), residues: 1280 helix: 1.14 (0.18), residues: 794 sheet: -1.30 (0.61), residues: 68 loop : 0.60 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 187 TYR 0.009 0.001 TYR H 77 PHE 0.012 0.001 PHE B 265 TRP 0.012 0.001 TRP H 63 HIS 0.005 0.001 HIS H 289 Details of bonding type rmsd covalent geometry : bond 0.00384 (14208) covalent geometry : angle 0.61899 (19904) hydrogen bonds : bond 0.06363 ( 759) hydrogen bonds : angle 4.17345 ( 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 101 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: G 28 MET cc_start: 0.8944 (mmm) cc_final: 0.8606 (mmp) REVERT: G 49 CYS cc_start: 0.8741 (m) cc_final: 0.8515 (t) outliers start: 5 outliers final: 2 residues processed: 99 average time/residue: 0.2192 time to fit residues: 32.8161 Evaluate side-chains 84 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain H residue 200 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 29 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.115831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.091952 restraints weight = 64772.740| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.17 r_work: 0.3127 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14208 Z= 0.156 Angle : 0.562 6.678 19904 Z= 0.341 Chirality : 0.036 0.125 2216 Planarity : 0.003 0.037 1984 Dihedral : 23.799 163.052 3320 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.19 % Allowed : 5.13 % Favored : 94.68 % 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: 1.65 (0.24), residues: 1280 helix: 1.66 (0.18), residues: 794 sheet: -1.51 (0.59), residues: 68 loop : 0.64 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 199 TYR 0.006 0.001 TYR H 77 PHE 0.008 0.001 PHE B 64 TRP 0.008 0.001 TRP G 52 HIS 0.003 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00329 (14208) covalent geometry : angle 0.56236 (19904) hydrogen bonds : bond 0.05252 ( 759) hydrogen bonds : angle 3.75938 ( 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 89 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.465 Fit side-chains REVERT: G 49 CYS cc_start: 0.8804 (m) cc_final: 0.8543 (t) outliers start: 2 outliers final: 1 residues processed: 89 average time/residue: 0.2078 time to fit residues: 28.2637 Evaluate side-chains 84 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER 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: 4.9990 chunk 50 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.110530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.086559 restraints weight = 64515.734| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.16 r_work: 0.3030 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14208 Z= 0.244 Angle : 0.624 6.915 19904 Z= 0.375 Chirality : 0.041 0.137 2216 Planarity : 0.004 0.035 1984 Dihedral : 23.997 163.587 3320 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.75 % Allowed : 6.90 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.24), residues: 1280 helix: 1.46 (0.18), residues: 792 sheet: -1.53 (0.59), residues: 64 loop : 0.01 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 297 TYR 0.011 0.001 TYR H 77 PHE 0.015 0.002 PHE B 64 TRP 0.012 0.002 TRP G 52 HIS 0.004 0.001 HIS H 289 Details of bonding type rmsd covalent geometry : bond 0.00536 (14208) covalent geometry : angle 0.62398 (19904) hydrogen bonds : bond 0.07609 ( 759) hydrogen bonds : angle 4.06316 ( 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 87 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.391 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 84 average time/residue: 0.2137 time to fit residues: 27.1111 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 : 0.463 ------------------------------------------------------------------------------- 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 124 ASN Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain H residue 289 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 73 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.112630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.088749 restraints weight = 64211.039| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.15 r_work: 0.3071 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14208 Z= 0.170 Angle : 0.570 6.587 19904 Z= 0.344 Chirality : 0.037 0.127 2216 Planarity : 0.003 0.031 1984 Dihedral : 23.930 163.244 3320 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.65 % Allowed : 7.84 % Favored : 91.51 % 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: 1.39 (0.24), residues: 1280 helix: 1.66 (0.18), residues: 792 sheet: -1.52 (0.60), residues: 64 loop : 0.03 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 121 TYR 0.008 0.001 TYR H 77 PHE 0.010 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 covalent geometry : bond 0.00365 (14208) covalent geometry : angle 0.56979 (19904) hydrogen bonds : bond 0.05833 ( 759) hydrogen bonds : angle 3.75347 ( 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: 7 poor density : 81 time to evaluate : 0.649 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 86 average time/residue: 0.2138 time to fit residues: 28.4907 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 : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 23 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 94 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.111652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.087780 restraints weight = 64232.705| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.13 r_work: 0.3059 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14208 Z= 0.196 Angle : 0.574 6.488 19904 Z= 0.346 Chirality : 0.038 0.131 2216 Planarity : 0.004 0.032 1984 Dihedral : 23.988 163.812 3320 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.93 % Allowed : 8.02 % Favored : 91.04 % 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: 1.68 (0.18), residues: 792 sheet: -1.57 (0.60), residues: 64 loop : -0.16 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 297 TYR 0.006 0.001 TYR B 324 PHE 0.012 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 covalent geometry : bond 0.00427 (14208) covalent geometry : angle 0.57361 (19904) hydrogen bonds : bond 0.06202 ( 759) hydrogen bonds : angle 3.78158 ( 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 94 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.580 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 90 average time/residue: 0.2025 time to fit residues: 28.1126 Evaluate side-chains 85 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 23 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 138 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 125 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.111800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.087986 restraints weight = 64081.718| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.12 r_work: 0.3061 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14208 Z= 0.185 Angle : 0.566 6.661 19904 Z= 0.340 Chirality : 0.037 0.130 2216 Planarity : 0.003 0.033 1984 Dihedral : 24.013 163.435 3320 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.75 % Allowed : 8.58 % 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: 1.37 (0.24), residues: 1280 helix: 1.78 (0.18), residues: 792 sheet: -1.86 (0.59), residues: 68 loop : -0.19 (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 0.011 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 covalent geometry : bond 0.00402 (14208) covalent geometry : angle 0.56604 (19904) hydrogen bonds : bond 0.05854 ( 759) hydrogen bonds : angle 3.69321 ( 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 87 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.596 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 85 average time/residue: 0.1983 time to fit residues: 25.7220 Evaluate side-chains 86 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 125 VAL 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: 2.9990 chunk 97 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.113425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.089602 restraints weight = 64192.092| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.13 r_work: 0.3100 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14208 Z= 0.153 Angle : 0.539 6.192 19904 Z= 0.325 Chirality : 0.036 0.128 2216 Planarity : 0.003 0.032 1984 Dihedral : 23.939 164.105 3320 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.84 % Allowed : 8.68 % Favored : 90.49 % 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: 1.58 (0.24), residues: 1280 helix: 1.97 (0.18), residues: 794 sheet: -1.90 (0.59), residues: 68 loop : -0.15 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 187 TYR 0.006 0.001 TYR B 324 PHE 0.008 0.001 PHE B 64 TRP 0.009 0.001 TRP G 52 HIS 0.002 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00327 (14208) covalent geometry : angle 0.53927 (19904) hydrogen bonds : bond 0.04957 ( 759) hydrogen bonds : angle 3.51179 ( 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 90 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.640 Fit side-chains REVERT: A 287 SER cc_start: 0.8820 (OUTLIER) cc_final: 0.8610 (t) REVERT: G 49 CYS cc_start: 0.8864 (m) cc_final: 0.8606 (t) outliers start: 9 outliers final: 8 residues processed: 88 average time/residue: 0.2007 time to fit residues: 27.2206 Evaluate side-chains 88 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 125 VAL 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: 3.9990 chunk 105 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.110921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.087016 restraints weight = 64333.140| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.12 r_work: 0.3044 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14208 Z= 0.213 Angle : 0.578 6.625 19904 Z= 0.346 Chirality : 0.039 0.133 2216 Planarity : 0.004 0.034 1984 Dihedral : 24.030 164.791 3320 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.75 % Allowed : 9.24 % Favored : 90.02 % 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: 1.34 (0.24), residues: 1280 helix: 1.82 (0.18), residues: 792 sheet: -1.98 (0.58), residues: 68 loop : -0.34 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 187 TYR 0.009 0.001 TYR B 324 PHE 0.012 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 covalent geometry : bond 0.00467 (14208) covalent geometry : angle 0.57830 (19904) hydrogen bonds : bond 0.06399 ( 759) hydrogen bonds : angle 3.75874 ( 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 88 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.568 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 86 average time/residue: 0.2061 time to fit residues: 27.0518 Evaluate side-chains 86 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 125 VAL 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: 5.9990 chunk 73 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 81 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 112 optimal weight: 0.3980 chunk 78 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.112380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.088549 restraints weight = 64138.671| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.12 r_work: 0.3072 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14208 Z= 0.164 Angle : 0.554 7.051 19904 Z= 0.333 Chirality : 0.036 0.130 2216 Planarity : 0.003 0.033 1984 Dihedral : 23.973 164.271 3320 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.75 % Allowed : 9.42 % Favored : 89.83 % 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: 1.51 (0.24), residues: 1280 helix: 1.96 (0.18), residues: 792 sheet: -1.92 (0.58), residues: 68 loop : -0.30 (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 B 324 PHE 0.010 0.001 PHE B 64 TRP 0.010 0.001 TRP G 52 HIS 0.002 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00350 (14208) covalent geometry : angle 0.55448 (19904) hydrogen bonds : bond 0.05372 ( 759) hydrogen bonds : angle 3.58246 ( 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 89 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.619 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 87 average time/residue: 0.2146 time to fit residues: 28.6420 Evaluate side-chains 86 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 125 VAL 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: 4.9990 chunk 65 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.111139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.087316 restraints weight = 63992.886| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.10 r_work: 0.3051 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14208 Z= 0.201 Angle : 0.572 7.062 19904 Z= 0.342 Chirality : 0.038 0.134 2216 Planarity : 0.004 0.034 1984 Dihedral : 24.032 165.150 3320 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.75 % Allowed : 9.51 % Favored : 89.74 % 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: 1.37 (0.24), residues: 1280 helix: 1.87 (0.18), residues: 792 sheet: -1.96 (0.58), residues: 68 loop : -0.40 (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 B 324 PHE 0.012 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 covalent geometry : bond 0.00439 (14208) covalent geometry : angle 0.57169 (19904) hydrogen bonds : bond 0.06120 ( 759) hydrogen bonds : angle 3.71410 ( 2036) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5736.88 seconds wall clock time: 98 minutes 13.76 seconds (5893.76 seconds total)