Starting phenix.real_space_refine on Sat Aug 23 13:42:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e14_27823/08_2025/8e14_27823.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e14_27823/08_2025/8e14_27823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e14_27823/08_2025/8e14_27823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e14_27823/08_2025/8e14_27823.map" model { file = "/net/cci-nas-00/data/ceres_data/8e14_27823/08_2025/8e14_27823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e14_27823/08_2025/8e14_27823.cif" } resolution = 3.36 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= 0.001 sd= 0.054 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 Zn 2 6.06 5 P 154 5.49 5 S 28 5.16 5 C 7398 2.51 5 N 2309 2.21 5 O 2551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12442 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2099 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 16, 'TRANS': 252} Chain: "B" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1687 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain: "C" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 400 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "D" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 400 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "E" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2099 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 16, 'TRANS': 252} Chain: "F" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1691 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "G" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 400 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "H" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 400 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "I" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 869 Classifications: {'DNA': 42} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 41} Chain: "J" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 445 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Chain: "K" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 318 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "L" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 869 Classifications: {'DNA': 42} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 41} Chain: "M" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 445 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Chain: "N" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 318 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 283 SG CYS A 37 51.205 29.371 68.936 1.00212.62 S ATOM 306 SG CYS A 40 52.839 32.147 70.998 1.00202.14 S ATOM 4869 SG CYS E 37 91.975 74.210 70.160 1.00216.70 S ATOM 4892 SG CYS E 40 91.930 70.341 70.223 1.00213.90 S Time building chain proxies: 2.79, per 1000 atoms: 0.22 Number of scatterers: 12442 At special positions: 0 Unit cell: (146.16, 107.88, 132.24, 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) Zn 2 29.99 S 28 16.00 P 154 15.00 O 2551 8.00 N 2309 7.00 C 7398 6.00 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: 1.07 Conformation dependent library (CDL) restraints added in 441.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 13 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 9 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 37 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 40 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 9 " pdb="ZN ZN E 301 " - pdb=" ND1 HIS E 13 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 40 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 37 " Number of angles added : 3 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 15 sheets defined 30.4% alpha, 14.4% beta 72 base pairs and 120 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 Processing helix chain 'A' and resid 15 through 21 Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 99 through 105 Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.540A pdb=" N GLU A 133 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP A 138 " --> pdb=" O TRP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 172 removed outlier: 3.892A pdb=" N ARG A 161 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 198 removed outlier: 3.534A pdb=" N ALA A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 214 removed outlier: 3.811A pdb=" N TRP A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 113 Processing helix chain 'B' and resid 128 through 139 removed outlier: 3.728A pdb=" N TRP B 138 " --> pdb=" O TRP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 153 Processing helix chain 'B' and resid 154 through 174 removed outlier: 3.574A pdb=" N ARG B 161 " --> pdb=" O GLU B 157 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 184 removed outlier: 3.579A pdb=" N LYS B 184 " --> pdb=" O PRO B 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 181 through 184' Processing helix chain 'B' and resid 185 through 198 removed outlier: 3.712A pdb=" N ALA B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 261 through 263 No H-bonds generated for 'chain 'B' and resid 261 through 263' Processing helix chain 'E' and resid 2 through 13 removed outlier: 3.679A pdb=" N ASP E 7 " --> pdb=" O ARG E 3 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR E 10 " --> pdb=" O LYS E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 24 Processing helix chain 'E' and resid 26 through 34 Processing helix chain 'E' and resid 99 through 113 removed outlier: 3.819A pdb=" N HIS E 103 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N TRP E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA E 106 " --> pdb=" O GLN E 102 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA E 110 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 139 Processing helix chain 'E' and resid 150 through 152 No H-bonds generated for 'chain 'E' and resid 150 through 152' Processing helix chain 'E' and resid 153 through 158 Processing helix chain 'E' and resid 158 through 172 removed outlier: 3.650A pdb=" N LEU E 162 " --> pdb=" O ARG E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 197 removed outlier: 3.700A pdb=" N ALA E 190 " --> pdb=" O GLY E 186 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN E 197 " --> pdb=" O MET E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 214 Processing helix chain 'F' and resid 98 through 113 removed outlier: 4.228A pdb=" N GLN F 102 " --> pdb=" O SER F 98 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N HIS F 103 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N HIS F 104 " --> pdb=" O ALA F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 139 removed outlier: 3.677A pdb=" N TRP F 138 " --> pdb=" O TRP F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 174 removed outlier: 4.297A pdb=" N ALA F 159 " --> pdb=" O MET F 155 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 199 removed outlier: 3.990A pdb=" N LYS F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 214 Processing helix chain 'F' and resid 263 through 265 No H-bonds generated for 'chain 'F' and resid 263 through 265' Processing helix chain 'G' and resid 263 through 265 No H-bonds generated for 'chain 'G' and resid 263 through 265' Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 65 Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 261 removed outlier: 3.948A pdb=" N GLY A 236 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL A 224 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 62 through 66 Processing sheet with id=AA4, first strand: chain 'B' and resid 118 through 119 removed outlier: 6.625A pdb=" N ILE B 118 " --> pdb=" O THR B 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 257 through 258 removed outlier: 5.022A pdb=" N GLY B 236 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL B 224 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 258 through 261 removed outlier: 6.790A pdb=" N TYR C 246 " --> pdb=" O TRP C 242 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N TRP C 242 " --> pdb=" O TYR C 246 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA C 248 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU C 232 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 228 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLY C 236 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N VAL C 224 " --> pdb=" O GLY C 236 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 258 through 261 removed outlier: 4.245A pdb=" N TRP D 237 " --> pdb=" O VAL D 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 61 through 67 Processing sheet with id=AA9, first strand: chain 'E' and resid 117 through 120 removed outlier: 6.175A pdb=" N ILE E 118 " --> pdb=" O THR E 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 226 through 227 removed outlier: 3.671A pdb=" N ILE E 226 " --> pdb=" O GLU E 234 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 237 through 241 removed outlier: 3.628A pdb=" N LEU E 240 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ALA E 248 " --> pdb=" O LEU E 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 88 through 91 removed outlier: 6.664A pdb=" N TRP F 61 " --> pdb=" O LYS F 119 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 223 through 224 removed outlier: 3.900A pdb=" N VAL F 260 " --> pdb=" O ALA F 247 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 239 through 241 removed outlier: 7.030A pdb=" N ALA G 248 " --> pdb=" O LEU G 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 224 through 225 287 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 173 hydrogen bonds 346 hydrogen bond angles 0 basepair planarities 72 basepair parallelities 120 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 2 1.15 - 1.32: 1693 1.32 - 1.48: 6230 1.48 - 1.65: 5099 1.65 - 1.82: 48 Bond restraints: 13072 Sorted by residual: bond pdb=" CG ASP C 253 " pdb=" OD1 ASP C 253 " ideal model delta sigma weight residual 1.249 1.529 -0.280 1.90e-02 2.77e+03 2.17e+02 bond pdb=" CG ASP E 255 " pdb=" OD2 ASP E 255 " ideal model delta sigma weight residual 1.249 1.516 -0.267 1.90e-02 2.77e+03 1.97e+02 bond pdb=" CG ASP E 255 " pdb=" OD1 ASP E 255 " ideal model delta sigma weight residual 1.249 0.983 0.266 1.90e-02 2.77e+03 1.96e+02 bond pdb=" CA VAL D 265 " pdb=" C VAL D 265 " ideal model delta sigma weight residual 1.522 1.660 -0.138 1.19e-02 7.06e+03 1.35e+02 bond pdb=" CG ASP C 253 " pdb=" OD2 ASP C 253 " ideal model delta sigma weight residual 1.249 1.037 0.212 1.90e-02 2.77e+03 1.25e+02 ... (remaining 13067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.30: 18414 12.30 - 24.61: 8 24.61 - 36.91: 0 36.91 - 49.22: 2 49.22 - 61.52: 2 Bond angle restraints: 18426 Sorted by residual: angle pdb=" CB ASP E 255 " pdb=" CG ASP E 255 " pdb=" OD1 ASP E 255 " ideal model delta sigma weight residual 118.40 179.92 -61.52 2.30e+00 1.89e-01 7.16e+02 angle pdb=" CB ASP C 253 " pdb=" CG ASP C 253 " pdb=" OD2 ASP C 253 " ideal model delta sigma weight residual 118.40 178.41 -60.01 2.30e+00 1.89e-01 6.81e+02 angle pdb=" CA ASP C 253 " pdb=" CB ASP C 253 " pdb=" CG ASP C 253 " ideal model delta sigma weight residual 112.60 94.33 18.27 1.00e+00 1.00e+00 3.34e+02 angle pdb=" OD1 ASP E 255 " pdb=" CG ASP E 255 " pdb=" OD2 ASP E 255 " ideal model delta sigma weight residual 122.90 80.17 42.73 2.40e+00 1.74e-01 3.17e+02 angle pdb=" OD1 ASP C 253 " pdb=" CG ASP C 253 " pdb=" OD2 ASP C 253 " ideal model delta sigma weight residual 122.90 80.68 42.22 2.40e+00 1.74e-01 3.10e+02 ... (remaining 18421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 6605 35.97 - 71.93: 765 71.93 - 107.90: 16 107.90 - 143.86: 7 143.86 - 179.83: 6 Dihedral angle restraints: 7399 sinusoidal: 4098 harmonic: 3301 Sorted by residual: dihedral pdb=" C VAL D 265 " pdb=" N VAL D 265 " pdb=" CA VAL D 265 " pdb=" CB VAL D 265 " ideal model delta harmonic sigma weight residual -122.00 -97.01 -24.99 0 2.50e+00 1.60e-01 1.00e+02 dihedral pdb=" CA PRO B 73 " pdb=" C PRO B 73 " pdb=" N ARG B 74 " pdb=" CA ARG B 74 " ideal model delta harmonic sigma weight residual 180.00 144.80 35.20 0 5.00e+00 4.00e-02 4.95e+01 dihedral pdb=" CA VAL E 101 " pdb=" C VAL E 101 " pdb=" N GLN E 102 " pdb=" CA GLN E 102 " ideal model delta harmonic sigma weight residual 180.00 149.36 30.64 0 5.00e+00 4.00e-02 3.76e+01 ... (remaining 7396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.616: 2034 0.616 - 1.231: 1 1.231 - 1.847: 0 1.847 - 2.462: 0 2.462 - 3.078: 1 Chirality restraints: 2036 Sorted by residual: chirality pdb=" CB VAL D 265 " pdb=" CA VAL D 265 " pdb=" CG1 VAL D 265 " pdb=" CG2 VAL D 265 " both_signs ideal model delta sigma weight residual False -2.63 0.45 -3.08 2.00e-01 2.50e+01 2.37e+02 chirality pdb=" CA VAL D 265 " pdb=" N VAL D 265 " pdb=" C VAL D 265 " pdb=" CB VAL D 265 " both_signs ideal model delta sigma weight residual False 2.44 3.37 -0.93 2.00e-01 2.50e+01 2.16e+01 chirality pdb=" CA ASP E 255 " pdb=" N ASP E 255 " pdb=" C ASP E 255 " pdb=" CB ASP E 255 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.42e+00 ... (remaining 2033 not shown) Planarity restraints: 1774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 233 " -0.045 2.00e-02 2.50e+03 4.83e-02 5.84e+01 pdb=" CG TRP H 233 " 0.127 2.00e-02 2.50e+03 pdb=" CD1 TRP H 233 " -0.069 2.00e-02 2.50e+03 pdb=" CD2 TRP H 233 " -0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP H 233 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP H 233 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP H 233 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 233 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 233 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP H 233 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 222 " -0.114 5.00e-02 4.00e+02 1.52e-01 3.69e+01 pdb=" N PRO D 223 " 0.261 5.00e-02 4.00e+02 pdb=" CA PRO D 223 " -0.077 5.00e-02 4.00e+02 pdb=" CD PRO D 223 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 232 " -0.023 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" CD GLU D 232 " 0.077 2.00e-02 2.50e+03 pdb=" OE1 GLU D 232 " -0.028 2.00e-02 2.50e+03 pdb=" OE2 GLU D 232 " -0.026 2.00e-02 2.50e+03 ... (remaining 1771 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 995 2.73 - 3.27: 12344 3.27 - 3.81: 22571 3.81 - 4.36: 24812 4.36 - 4.90: 38546 Nonbonded interactions: 99268 Sorted by model distance: nonbonded pdb=" NE2 HIS B 93 " pdb=" O ARG B 95 " model vdw 2.182 3.120 nonbonded pdb=" OD1 ASP B 64 " pdb=" N PHE B 65 " model vdw 2.233 3.120 nonbonded pdb=" N GLU G 229 " pdb=" OE1 GLU G 229 " model vdw 2.238 3.120 nonbonded pdb=" O ARG H 227 " pdb=" NZ LYS H 264 " model vdw 2.242 3.120 nonbonded pdb=" O ARG H 244 " pdb=" OG SER H 262 " model vdw 2.257 3.040 ... (remaining 99263 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 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 57 through 269) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'K' selection = chain 'N' } 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: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.540 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 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 : 0.007 0.280 13080 Z= 0.346 Angle : 1.125 61.523 18429 Z= 0.580 Chirality : 0.083 3.078 2036 Planarity : 0.006 0.152 1774 Dihedral : 24.724 179.828 5263 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.73 % Favored : 82.27 % Rotamer: Outliers : 0.41 % Allowed : 36.16 % Favored : 63.43 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 aren not related in a simple way. whole: -2.84 (0.24), residues: 1145 helix: 0.29 (0.31), residues: 300 sheet: -1.47 (0.36), residues: 183 loop : -3.26 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG H 244 TYR 0.017 0.001 TYR E 246 PHE 0.005 0.001 PHE A 199 TRP 0.127 0.001 TRP H 233 HIS 0.006 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00689 (13072) covalent geometry : angle 1.12410 (18426) hydrogen bonds : bond 0.07794 ( 460) hydrogen bonds : angle 4.22499 ( 1162) metal coordination : bond 0.00371 ( 8) metal coordination : angle 3.28923 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 GLU cc_start: 0.9536 (OUTLIER) cc_final: 0.9218 (pm20) outliers start: 4 outliers final: 1 residues processed: 61 average time/residue: 0.1482 time to fit residues: 12.2461 Evaluate side-chains 60 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain E residue 4 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.052246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.036007 restraints weight = 102343.473| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 4.82 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 13080 Z= 0.262 Angle : 0.712 8.849 18429 Z= 0.392 Chirality : 0.043 0.215 2036 Planarity : 0.005 0.075 1774 Dihedral : 27.100 176.583 3033 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.78 % Favored : 81.22 % Rotamer: Outliers : 5.58 % Allowed : 32.44 % Favored : 61.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -3.08 (0.23), residues: 1145 helix: -0.06 (0.30), residues: 302 sheet: -1.87 (0.35), residues: 186 loop : -3.25 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 244 TYR 0.019 0.002 TYR E 246 PHE 0.012 0.001 PHE A 199 TRP 0.010 0.001 TRP C 242 HIS 0.006 0.001 HIS E 9 Details of bonding type rmsd covalent geometry : bond 0.00581 (13072) covalent geometry : angle 0.71065 (18426) hydrogen bonds : bond 0.06140 ( 460) hydrogen bonds : angle 4.46060 ( 1162) metal coordination : bond 0.00723 ( 8) metal coordination : angle 3.40355 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 59 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8615 (mm) REVERT: B 64 ASP cc_start: 0.8584 (t0) cc_final: 0.8179 (t0) REVERT: C 225 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.9063 (ttpp) REVERT: E 193 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.7567 (mpt) REVERT: F 64 ASP cc_start: 0.7988 (t0) cc_final: 0.7718 (t0) REVERT: G 225 LYS cc_start: 0.9271 (mmmm) cc_final: 0.8899 (mmmm) REVERT: H 233 TRP cc_start: 0.8723 (m100) cc_final: 0.8439 (m100) outliers start: 54 outliers final: 30 residues processed: 106 average time/residue: 0.1343 time to fit residues: 19.8921 Evaluate side-chains 89 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 56 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 103 HIS Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 268 ASP Chi-restraints excluded: chain H residue 253 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 40 optimal weight: 0.0670 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 87 optimal weight: 10.0000 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.053729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.037283 restraints weight = 101571.285| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 5.17 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13080 Z= 0.143 Angle : 0.650 10.364 18429 Z= 0.355 Chirality : 0.041 0.214 2036 Planarity : 0.005 0.058 1774 Dihedral : 26.950 179.386 3030 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.68 % Favored : 83.32 % Rotamer: Outliers : 5.06 % Allowed : 32.13 % Favored : 62.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 aren not related in a simple way. whole: -2.79 (0.24), residues: 1145 helix: 0.18 (0.31), residues: 305 sheet: -1.42 (0.36), residues: 175 loop : -3.15 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 227 TYR 0.016 0.001 TYR E 246 PHE 0.006 0.001 PHE A 199 TRP 0.013 0.001 TRP D 237 HIS 0.005 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00319 (13072) covalent geometry : angle 0.64950 (18426) hydrogen bonds : bond 0.03677 ( 460) hydrogen bonds : angle 4.16686 ( 1162) metal coordination : bond 0.01106 ( 8) metal coordination : angle 2.73320 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 65 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8467 (mm) REVERT: B 64 ASP cc_start: 0.8559 (t0) cc_final: 0.8200 (t70) REVERT: F 64 ASP cc_start: 0.7967 (t0) cc_final: 0.7525 (t0) REVERT: G 225 LYS cc_start: 0.9223 (mmmm) cc_final: 0.8671 (mmmm) REVERT: H 227 ARG cc_start: 0.7761 (mtt90) cc_final: 0.7289 (mmm160) REVERT: H 233 TRP cc_start: 0.8908 (m100) cc_final: 0.8439 (m100) outliers start: 49 outliers final: 28 residues processed: 111 average time/residue: 0.1545 time to fit residues: 23.3726 Evaluate side-chains 89 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 60 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 103 HIS Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 238 ASN Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 268 ASP Chi-restraints excluded: chain H residue 253 ASP Chi-restraints excluded: chain H residue 264 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.053515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.037095 restraints weight = 100831.980| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 5.13 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13080 Z= 0.156 Angle : 0.647 11.090 18429 Z= 0.353 Chirality : 0.041 0.209 2036 Planarity : 0.005 0.058 1774 Dihedral : 26.899 177.777 3030 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.68 % Favored : 83.32 % Rotamer: Outliers : 5.37 % Allowed : 32.02 % Favored : 62.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 aren not related in a simple way. whole: -2.75 (0.24), residues: 1145 helix: 0.15 (0.30), residues: 316 sheet: -1.59 (0.35), residues: 190 loop : -3.10 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 227 TYR 0.017 0.001 TYR E 246 PHE 0.007 0.001 PHE A 199 TRP 0.013 0.001 TRP D 237 HIS 0.005 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00349 (13072) covalent geometry : angle 0.64618 (18426) hydrogen bonds : bond 0.04000 ( 460) hydrogen bonds : angle 4.14447 ( 1162) metal coordination : bond 0.00582 ( 8) metal coordination : angle 2.83957 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 64 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8770 (tpt-90) REVERT: B 60 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8542 (mm) REVERT: B 64 ASP cc_start: 0.8647 (t0) cc_final: 0.8276 (t70) REVERT: F 64 ASP cc_start: 0.7910 (t0) cc_final: 0.7382 (t0) REVERT: F 114 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8612 (ttm-80) REVERT: G 225 LYS cc_start: 0.9212 (mmmm) cc_final: 0.8723 (mmmm) REVERT: H 227 ARG cc_start: 0.7833 (mtt90) cc_final: 0.7319 (mmm160) outliers start: 52 outliers final: 31 residues processed: 111 average time/residue: 0.1520 time to fit residues: 22.9093 Evaluate side-chains 93 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 59 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 103 HIS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 238 ASN Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 253 ASP Chi-restraints excluded: chain G residue 268 ASP Chi-restraints excluded: chain H residue 256 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 104 optimal weight: 0.0070 chunk 42 optimal weight: 4.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN E 238 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.052706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.036127 restraints weight = 102583.357| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 5.49 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13080 Z= 0.212 Angle : 0.685 9.398 18429 Z= 0.374 Chirality : 0.043 0.231 2036 Planarity : 0.005 0.053 1774 Dihedral : 26.963 175.568 3030 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.64 % Favored : 82.36 % Rotamer: Outliers : 6.10 % Allowed : 31.82 % Favored : 62.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -2.88 (0.24), residues: 1145 helix: 0.06 (0.30), residues: 316 sheet: -1.79 (0.34), residues: 191 loop : -3.14 (0.22), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 244 TYR 0.017 0.001 TYR E 246 PHE 0.010 0.001 PHE A 199 TRP 0.014 0.001 TRP D 237 HIS 0.005 0.001 HIS E 9 Details of bonding type rmsd covalent geometry : bond 0.00474 (13072) covalent geometry : angle 0.68420 (18426) hydrogen bonds : bond 0.05084 ( 460) hydrogen bonds : angle 4.30671 ( 1162) metal coordination : bond 0.00348 ( 8) metal coordination : angle 2.67787 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 58 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8609 (mm) REVERT: B 64 ASP cc_start: 0.8667 (t0) cc_final: 0.8229 (t70) REVERT: F 64 ASP cc_start: 0.7909 (t0) cc_final: 0.7437 (t0) REVERT: F 114 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8507 (ttm-80) REVERT: G 225 LYS cc_start: 0.9288 (mmmm) cc_final: 0.8851 (mmmm) outliers start: 59 outliers final: 37 residues processed: 112 average time/residue: 0.1452 time to fit residues: 22.1198 Evaluate side-chains 94 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 55 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 65 PHE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 103 HIS Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 161 ARG Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 238 ASN Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 268 ASP Chi-restraints excluded: chain H residue 256 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 92 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.0670 chunk 44 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.053209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.037015 restraints weight = 101141.871| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 4.83 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13080 Z= 0.159 Angle : 0.662 9.570 18429 Z= 0.360 Chirality : 0.042 0.215 2036 Planarity : 0.005 0.050 1774 Dihedral : 26.932 177.100 3030 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.03 % Favored : 82.97 % Rotamer: Outliers : 5.27 % Allowed : 31.92 % Favored : 62.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -2.75 (0.24), residues: 1145 helix: 0.18 (0.30), residues: 316 sheet: -1.64 (0.34), residues: 198 loop : -3.11 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 227 TYR 0.016 0.001 TYR E 246 PHE 0.008 0.001 PHE A 199 TRP 0.016 0.001 TRP D 237 HIS 0.004 0.001 HIS E 9 Details of bonding type rmsd covalent geometry : bond 0.00358 (13072) covalent geometry : angle 0.66090 (18426) hydrogen bonds : bond 0.03950 ( 460) hydrogen bonds : angle 4.22655 ( 1162) metal coordination : bond 0.00590 ( 8) metal coordination : angle 2.58349 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 61 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8184 (mtp180) REVERT: A 155 MET cc_start: 0.7711 (mtt) cc_final: 0.7372 (mtt) REVERT: A 158 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8734 (tpt-90) REVERT: B 64 ASP cc_start: 0.8767 (t70) cc_final: 0.8351 (t70) REVERT: F 64 ASP cc_start: 0.7978 (t0) cc_final: 0.7481 (t0) REVERT: F 114 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8591 (ttm-80) REVERT: F 266 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8587 (mmtm) REVERT: G 225 LYS cc_start: 0.9278 (mmmm) cc_final: 0.8845 (mmmm) REVERT: G 256 LYS cc_start: 0.8931 (mtmm) cc_final: 0.8575 (mtmm) outliers start: 51 outliers final: 40 residues processed: 107 average time/residue: 0.1470 time to fit residues: 21.2250 Evaluate side-chains 100 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 56 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 103 HIS Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 178 LYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 161 ARG Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 238 ASN Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 266 LYS Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 268 ASP Chi-restraints excluded: chain H residue 256 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 48 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 55 optimal weight: 30.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN F 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.051207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.034773 restraints weight = 103540.787| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 5.60 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 13080 Z= 0.344 Angle : 0.794 11.442 18429 Z= 0.432 Chirality : 0.046 0.287 2036 Planarity : 0.006 0.067 1774 Dihedral : 27.296 174.687 3030 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.39 % Favored : 80.61 % Rotamer: Outliers : 6.82 % Allowed : 31.10 % Favored : 62.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -3.10 (0.23), residues: 1145 helix: -0.23 (0.29), residues: 300 sheet: -1.86 (0.34), residues: 179 loop : -3.17 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 244 TYR 0.023 0.002 TYR E 246 PHE 0.018 0.002 PHE A 199 TRP 0.016 0.002 TRP D 237 HIS 0.006 0.001 HIS E 9 Details of bonding type rmsd covalent geometry : bond 0.00760 (13072) covalent geometry : angle 0.79316 (18426) hydrogen bonds : bond 0.07900 ( 460) hydrogen bonds : angle 4.76080 ( 1162) metal coordination : bond 0.01462 ( 8) metal coordination : angle 2.16908 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 56 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.7852 (mtt) cc_final: 0.7558 (mtt) REVERT: B 64 ASP cc_start: 0.8801 (t70) cc_final: 0.8391 (t70) REVERT: E 193 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.7373 (mpt) REVERT: F 64 ASP cc_start: 0.8381 (t0) cc_final: 0.7953 (t0) REVERT: F 114 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8519 (ttp80) REVERT: G 225 LYS cc_start: 0.9370 (mmmm) cc_final: 0.9002 (mmmm) REVERT: G 256 LYS cc_start: 0.9005 (mtmm) cc_final: 0.8724 (mtmm) outliers start: 66 outliers final: 53 residues processed: 118 average time/residue: 0.1379 time to fit residues: 22.1797 Evaluate side-chains 109 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 54 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 65 PHE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 103 HIS Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 178 LYS Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 161 ARG Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 238 ASN Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 268 ASP Chi-restraints excluded: chain H residue 256 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 122 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.052905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.036817 restraints weight = 101276.866| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 4.86 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13080 Z= 0.152 Angle : 0.691 9.636 18429 Z= 0.373 Chirality : 0.043 0.248 2036 Planarity : 0.005 0.047 1774 Dihedral : 27.150 178.479 3030 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.94 % Favored : 83.06 % Rotamer: Outliers : 5.17 % Allowed : 32.44 % Favored : 62.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 aren not related in a simple way. whole: -2.81 (0.23), residues: 1145 helix: 0.10 (0.30), residues: 304 sheet: -1.71 (0.35), residues: 179 loop : -3.05 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 227 TYR 0.014 0.001 TYR E 246 PHE 0.007 0.001 PHE A 199 TRP 0.022 0.001 TRP D 237 HIS 0.004 0.001 HIS E 9 Details of bonding type rmsd covalent geometry : bond 0.00342 (13072) covalent geometry : angle 0.69059 (18426) hydrogen bonds : bond 0.03874 ( 460) hydrogen bonds : angle 4.32620 ( 1162) metal coordination : bond 0.01014 ( 8) metal coordination : angle 2.39489 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 65 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 ASP cc_start: 0.8867 (t70) cc_final: 0.8457 (t70) REVERT: F 64 ASP cc_start: 0.8255 (t0) cc_final: 0.7868 (t0) REVERT: F 71 MET cc_start: 0.8681 (tpt) cc_final: 0.8389 (tpt) REVERT: F 114 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8542 (ttm-80) REVERT: G 225 LYS cc_start: 0.9331 (mmmm) cc_final: 0.8952 (mmmm) REVERT: G 256 LYS cc_start: 0.8883 (mtmm) cc_final: 0.8487 (mtmm) outliers start: 50 outliers final: 41 residues processed: 111 average time/residue: 0.1463 time to fit residues: 22.4616 Evaluate side-chains 102 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 60 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 65 PHE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 103 HIS Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 161 ARG Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 238 ASN Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 268 ASP Chi-restraints excluded: chain H residue 256 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 93 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 78 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.052455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.036230 restraints weight = 102735.950| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 5.04 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13080 Z= 0.196 Angle : 0.711 11.384 18429 Z= 0.383 Chirality : 0.043 0.249 2036 Planarity : 0.005 0.047 1774 Dihedral : 27.159 175.864 3030 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.55 % Favored : 82.45 % Rotamer: Outliers : 4.65 % Allowed : 32.85 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -2.87 (0.23), residues: 1145 helix: 0.02 (0.29), residues: 316 sheet: -1.63 (0.35), residues: 177 loop : -3.15 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 227 TYR 0.018 0.001 TYR E 246 PHE 0.009 0.001 PHE A 199 TRP 0.020 0.001 TRP D 237 HIS 0.005 0.001 HIS E 9 Details of bonding type rmsd covalent geometry : bond 0.00438 (13072) covalent geometry : angle 0.71040 (18426) hydrogen bonds : bond 0.04700 ( 460) hydrogen bonds : angle 4.44067 ( 1162) metal coordination : bond 0.00242 ( 8) metal coordination : angle 2.50918 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 59 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 ASP cc_start: 0.8818 (t70) cc_final: 0.8396 (t70) REVERT: F 64 ASP cc_start: 0.8331 (t0) cc_final: 0.7933 (t0) REVERT: F 71 MET cc_start: 0.8426 (tpt) cc_final: 0.8134 (tpt) REVERT: G 225 LYS cc_start: 0.9323 (mmmm) cc_final: 0.8942 (mmmm) REVERT: G 256 LYS cc_start: 0.8853 (mtmm) cc_final: 0.8448 (mtmm) outliers start: 45 outliers final: 39 residues processed: 101 average time/residue: 0.1387 time to fit residues: 19.6186 Evaluate side-chains 97 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 58 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 65 PHE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 103 HIS Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 161 ARG Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 238 ASN Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 268 ASP Chi-restraints excluded: chain H residue 256 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 0.1980 chunk 121 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 86 optimal weight: 0.3980 chunk 122 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.053282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.036992 restraints weight = 101538.980| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 5.18 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13080 Z= 0.148 Angle : 0.699 11.735 18429 Z= 0.374 Chirality : 0.042 0.244 2036 Planarity : 0.005 0.048 1774 Dihedral : 27.061 178.019 3030 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.03 % Favored : 82.97 % Rotamer: Outliers : 4.65 % Allowed : 32.85 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 aren not related in a simple way. whole: -2.68 (0.24), residues: 1145 helix: 0.11 (0.30), residues: 311 sheet: -1.36 (0.37), residues: 162 loop : -3.00 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 227 TYR 0.015 0.001 TYR E 246 PHE 0.005 0.001 PHE A 199 TRP 0.021 0.001 TRP D 237 HIS 0.004 0.001 HIS E 9 Details of bonding type rmsd covalent geometry : bond 0.00334 (13072) covalent geometry : angle 0.69807 (18426) hydrogen bonds : bond 0.03638 ( 460) hydrogen bonds : angle 4.31166 ( 1162) metal coordination : bond 0.00920 ( 8) metal coordination : angle 2.72015 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 65 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 ASP cc_start: 0.8900 (t70) cc_final: 0.8492 (t70) REVERT: C 266 LYS cc_start: 0.9196 (ttpt) cc_final: 0.8941 (mtmt) REVERT: D 244 ARG cc_start: 0.7914 (mpt180) cc_final: 0.5768 (mmp-170) REVERT: F 64 ASP cc_start: 0.8235 (t0) cc_final: 0.7859 (t0) REVERT: F 71 MET cc_start: 0.8777 (tpt) cc_final: 0.8493 (tpt) REVERT: F 91 THR cc_start: 0.8742 (OUTLIER) cc_final: 0.8396 (p) REVERT: G 225 LYS cc_start: 0.9297 (mmmm) cc_final: 0.8895 (mmmm) REVERT: G 256 LYS cc_start: 0.8763 (mtmm) cc_final: 0.8368 (mtmm) outliers start: 45 outliers final: 35 residues processed: 107 average time/residue: 0.1504 time to fit residues: 22.0399 Evaluate side-chains 98 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 62 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 65 PHE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 103 HIS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 161 ARG Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 238 ASN Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 268 ASP Chi-restraints excluded: chain H residue 256 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 42 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 97 optimal weight: 0.0670 chunk 50 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 72 optimal weight: 0.0070 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.053857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.037555 restraints weight = 101267.159| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 5.79 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13080 Z= 0.145 Angle : 0.703 11.634 18429 Z= 0.375 Chirality : 0.042 0.236 2036 Planarity : 0.005 0.047 1774 Dihedral : 26.973 177.908 3030 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.68 % Favored : 83.32 % Rotamer: Outliers : 3.62 % Allowed : 33.57 % Favored : 62.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 aren not related in a simple way. whole: -2.59 (0.24), residues: 1145 helix: 0.16 (0.31), residues: 315 sheet: -1.30 (0.37), residues: 173 loop : -2.97 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B 158 TYR 0.016 0.001 TYR E 246 PHE 0.004 0.001 PHE F 176 TRP 0.023 0.001 TRP D 237 HIS 0.004 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00329 (13072) covalent geometry : angle 0.70249 (18426) hydrogen bonds : bond 0.03394 ( 460) hydrogen bonds : angle 4.19115 ( 1162) metal coordination : bond 0.01022 ( 8) metal coordination : angle 2.87699 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2857.78 seconds wall clock time: 49 minutes 58.77 seconds (2998.77 seconds total)