Starting phenix.real_space_refine on Fri Jul 3 05:47:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8e14_27823/07_2026/8e14_27823.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e14_27823/07_2026/8e14_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8e14_27823/07_2026/8e14_27823.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8e14_27823/07_2026/8e14_27823.cif" model { file = "/net/cci-nas-00/data/ceres_data/8e14_27823/07_2026/8e14_27823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e14_27823/07_2026/8e14_27823.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e14_27823/07_2026/8e14_27823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e14_27823/07_2026/8e14_27823.map" } 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-dev-6108/lib/python3.11/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: 3.05, per 1000 atoms: 0.25 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: 1.04 Conformation dependent library (CDL) restraints added in 486.5 milliseconds 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: 1.81 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: 2.42 Time building geometry restraints manager: 1.43 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: 2.570 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.710 Find NCS groups from input model: 0.200 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:1.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.280 13080 Z= 0.501 Angle : 1.180 61.523 18429 Z= 0.726 Chirality : 0.086 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 are 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/Z covalent geometry : bond 0.00753 / 0.50 (13072) covalent geometry : angle 1.17968 / 0.73 (18426) hydrogen bonds : bond 0.07794 / 5.56 ( 460) hydrogen bonds : angle 4.22499 / 2.90 ( 1162) metal coordination : bond 0.00371 / 0.21 ( 8) metal coordination : angle 3.28923 / 2.55 ( 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 : 0.408 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: 0.1563 time to fit residues: 13.0278 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 : 0.402 ------------------------------------------------------------------------------- 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: 5.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 123 optimal weight: 30.0000 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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 = 0.3597 r_free = 0.3597 target = 0.052653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.036356 restraints weight = 102046.350| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 4.93 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.0682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13080 Z= 0.255 Angle : 0.747 8.612 18429 Z= 0.418 Chirality : 0.048 0.272 2036 Planarity : 0.005 0.074 1774 Dihedral : 27.189 179.360 3033 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.17 % Favored : 81.83 % Rotamer: Outliers : 4.24 % Allowed : 32.64 % Favored : 63.12 % 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 are not related in a simple way. whole: -3.05 (0.23), residues: 1145 helix: 0.00 (0.30), residues: 302 sheet: -1.65 (0.36), residues: 173 loop : -3.31 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 244 TYR 0.019 0.002 TYR E 246 PHE 0.012 0.001 PHE A 199 TRP 0.017 0.001 TRP H 233 HIS 0.009 0.001 HIS B 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.25 (13072) covalent geometry : angle 0.74572 / 0.42 (18426) hydrogen bonds : bond 0.06039 / 4.19 ( 460) hydrogen bonds : angle 4.39971 / 3.03 ( 1162) metal coordination : bond 0.01117 / 0.62 ( 8) metal coordination : angle 3.06624 / 2.27 ( 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 102 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 61 time to evaluate : 0.492 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 60 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8510 (mm) REVERT: B 64 ASP cc_start: 0.8610 (t0) cc_final: 0.8261 (t0) REVERT: F 64 ASP cc_start: 0.7967 (t0) cc_final: 0.7763 (t0) outliers start: 41 outliers final: 23 residues processed: 97 average time/residue: 0.1324 time to fit residues: 18.0860 Evaluate side-chains 82 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 265 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 226 ILE 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 265 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 97 THR 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 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 253 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 104 optimal weight: 0.2980 chunk 40 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 87 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 HIS ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.053690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.037317 restraints weight = 101495.235| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 4.97 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13080 Z= 0.142 Angle : 0.685 9.540 18429 Z= 0.384 Chirality : 0.047 0.291 2036 Planarity : 0.005 0.057 1774 Dihedral : 27.109 178.821 3030 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.42 % Favored : 83.58 % Rotamer: Outliers : 5.37 % Allowed : 31.20 % Favored : 63.43 % 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 are not related in a simple way. whole: -2.79 (0.24), residues: 1145 helix: 0.25 (0.31), residues: 301 sheet: -1.55 (0.37), residues: 173 loop : -3.13 (0.22), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 263 TYR 0.019 0.001 TYR E 246 PHE 0.010 0.001 PHE A 65 TRP 0.025 0.001 TRP H 233 HIS 0.005 0.001 HIS B 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (13072) covalent geometry : angle 0.68391 / 0.38 (18426) hydrogen bonds : bond 0.04102 / 2.78 ( 460) hydrogen bonds : angle 4.20783 / 2.87 ( 1162) metal coordination : bond 0.01067 / 0.63 ( 8) metal coordination : angle 2.57743 / 2.05 ( 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 118 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 66 time to evaluate : 0.455 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: B 64 ASP cc_start: 0.8547 (t0) cc_final: 0.8065 (t0) REVERT: B 163 LEU cc_start: 0.9745 (OUTLIER) cc_final: 0.9469 (pp) REVERT: F 64 ASP cc_start: 0.7822 (t0) cc_final: 0.7399 (t0) REVERT: F 114 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8666 (ttm-80) REVERT: G 225 LYS cc_start: 0.9267 (mmmm) cc_final: 0.8705 (mmmm) outliers start: 52 outliers final: 29 residues processed: 113 average time/residue: 0.1230 time to fit residues: 19.6694 Evaluate side-chains 91 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 60 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE 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 155 MET 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 163 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 265 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 196 LEU Chi-restraints excluded: chain E residue 198 HIS 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 241 VAL Chi-restraints excluded: chain F residue 265 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 46 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 20 optimal weight: 0.3980 chunk 105 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.053666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.037363 restraints weight = 100823.928| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 4.93 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13080 Z= 0.142 Angle : 0.683 10.850 18429 Z= 0.379 Chirality : 0.047 0.289 2036 Planarity : 0.005 0.049 1774 Dihedral : 27.097 177.174 3030 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.03 % Favored : 82.97 % Rotamer: Outliers : 4.96 % Allowed : 31.61 % Favored : 63.43 % 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 are not related in a simple way. whole: -2.80 (0.24), residues: 1145 helix: 0.14 (0.31), residues: 316 sheet: -1.54 (0.36), residues: 181 loop : -3.16 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 227 TYR 0.017 0.001 TYR E 246 PHE 0.008 0.001 PHE A 65 TRP 0.019 0.001 TRP H 233 HIS 0.004 0.001 HIS E 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 (13072) covalent geometry : angle 0.68195 / 0.38 (18426) hydrogen bonds : bond 0.04100 / 2.80 ( 460) hydrogen bonds : angle 4.18648 / 2.86 ( 1162) metal coordination : bond 0.00726 / 0.42 ( 8) metal coordination : angle 2.56167 / 1.84 ( 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 112 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 64 time to evaluate : 0.455 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: 0.8534 (t70) cc_final: 0.8148 (t70) REVERT: B 163 LEU cc_start: 0.9745 (OUTLIER) cc_final: 0.9470 (pp) REVERT: F 64 ASP cc_start: 0.7838 (t0) cc_final: 0.7306 (t0) REVERT: F 114 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8686 (ttm-80) REVERT: G 225 LYS cc_start: 0.9233 (mmmm) cc_final: 0.8737 (mmmm) outliers start: 48 outliers final: 35 residues processed: 106 average time/residue: 0.1421 time to fit residues: 20.7931 Evaluate side-chains 99 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 62 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 155 MET 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 163 LEU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain D residue 254 THR 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 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 170 LEU Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 230 THR 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 254 THR Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 268 ASP Chi-restraints excluded: chain H residue 253 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 9.9990 chunk 59 optimal weight: 0.1980 chunk 106 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 117 optimal weight: 30.0000 chunk 97 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 104 optimal weight: 0.0770 chunk 42 optimal weight: 4.9990 overall best weight: 2.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.052983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.036635 restraints weight = 102330.570| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 5.02 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13080 Z= 0.183 Angle : 0.691 9.438 18429 Z= 0.385 Chirality : 0.047 0.289 2036 Planarity : 0.005 0.046 1774 Dihedral : 27.151 179.414 3030 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.64 % Favored : 82.36 % Rotamer: Outliers : 5.48 % Allowed : 32.13 % Favored : 62.40 % 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 are not related in a simple way. whole: -2.91 (0.24), residues: 1145 helix: 0.09 (0.30), residues: 316 sheet: -1.79 (0.34), residues: 195 loop : -3.21 (0.22), residues: 634 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 0.011 0.001 PHE A 199 TRP 0.025 0.001 TRP H 233 HIS 0.005 0.001 HIS E 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.18 (13072) covalent geometry : angle 0.69061 / 0.38 (18426) hydrogen bonds : bond 0.04993 / 3.46 ( 460) hydrogen bonds : angle 4.26521 / 2.93 ( 1162) metal coordination : bond 0.00308 / 0.13 ( 8) metal coordination : angle 2.75547 / 1.78 ( 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 115 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 62 time to evaluate : 0.364 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: B 64 ASP cc_start: 0.8663 (t70) cc_final: 0.8251 (t70) REVERT: D 244 ARG cc_start: 0.8300 (mpt180) cc_final: 0.7994 (mpt180) REVERT: F 64 ASP cc_start: 0.7806 (t0) cc_final: 0.7283 (t0) REVERT: F 266 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8711 (mmtm) REVERT: G 225 LYS cc_start: 0.9241 (mmmm) cc_final: 0.8761 (mmmm) outliers start: 53 outliers final: 35 residues processed: 110 average time/residue: 0.1382 time to fit residues: 21.1179 Evaluate side-chains 95 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 59 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 226 ILE Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 265 VAL 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 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 114 ARG Chi-restraints excluded: chain F residue 170 LEU 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 F residue 266 LYS Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 268 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 92 optimal weight: 2.9990 chunk 112 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.053094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.036775 restraints weight = 101729.653| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 4.93 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13080 Z= 0.166 Angle : 0.696 9.340 18429 Z= 0.386 Chirality : 0.047 0.293 2036 Planarity : 0.005 0.043 1774 Dihedral : 27.169 179.594 3030 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.47 % Favored : 82.53 % Rotamer: Outliers : 5.27 % Allowed : 32.44 % Favored : 62.29 % 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 are not related in a simple way. whole: -2.88 (0.24), residues: 1145 helix: 0.11 (0.30), residues: 316 sheet: -1.79 (0.34), residues: 199 loop : -3.19 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 227 TYR 0.017 0.001 TYR E 246 PHE 0.009 0.001 PHE A 199 TRP 0.030 0.001 TRP H 233 HIS 0.005 0.001 HIS E 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.17 (13072) covalent geometry : angle 0.69586 / 0.39 (18426) hydrogen bonds : bond 0.04610 / 3.19 ( 460) hydrogen bonds : angle 4.28061 / 2.94 ( 1162) metal coordination : bond 0.00313 / 0.16 ( 8) metal coordination : angle 2.37482 / 1.64 ( 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 114 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 63 time to evaluate : 0.322 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: A 155 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7394 (mtt) REVERT: B 64 ASP cc_start: 0.8604 (t70) cc_final: 0.8164 (t70) REVERT: D 244 ARG cc_start: 0.8285 (mpt180) cc_final: 0.7981 (mpt180) REVERT: F 64 ASP cc_start: 0.7900 (t0) cc_final: 0.7392 (t0) REVERT: G 225 LYS cc_start: 0.9252 (mmmm) cc_final: 0.8812 (mmmm) outliers start: 51 outliers final: 41 residues processed: 106 average time/residue: 0.1370 time to fit residues: 19.9339 Evaluate side-chains 101 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 59 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 155 MET 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 224 VAL 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 254 THR Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 265 VAL 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 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 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 240 LEU 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 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: 2.9990 chunk 103 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.052342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.036085 restraints weight = 101443.926| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 4.79 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 13080 Z= 0.239 Angle : 0.741 10.060 18429 Z= 0.408 Chirality : 0.048 0.290 2036 Planarity : 0.005 0.060 1774 Dihedral : 27.262 178.391 3030 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.43 % Favored : 81.57 % Rotamer: Outliers : 6.71 % Allowed : 31.71 % Favored : 61.57 % 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 are not related in a simple way. whole: -3.01 (0.23), residues: 1145 helix: -0.05 (0.29), residues: 312 sheet: -1.91 (0.34), residues: 189 loop : -3.19 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 227 TYR 0.018 0.002 TYR E 246 PHE 0.015 0.001 PHE A 199 TRP 0.020 0.001 TRP B 233 HIS 0.006 0.001 HIS E 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.24 (13072) covalent geometry : angle 0.73993 / 0.41 (18426) hydrogen bonds : bond 0.06099 / 4.25 ( 460) hydrogen bonds : angle 4.55613 / 3.16 ( 1162) metal coordination : bond 0.00720 / 0.37 ( 8) metal coordination : angle 2.42326 / 1.58 ( 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 128 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 63 time to evaluate : 0.388 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: A 155 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7469 (mtt) REVERT: B 64 ASP cc_start: 0.8722 (t70) cc_final: 0.8251 (t70) REVERT: F 64 ASP cc_start: 0.8059 (t0) cc_final: 0.7574 (t0) REVERT: F 114 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8585 (ttm-80) REVERT: F 266 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8437 (mptt) REVERT: G 225 LYS cc_start: 0.9276 (mmmm) cc_final: 0.8862 (mmmm) outliers start: 65 outliers final: 49 residues processed: 119 average time/residue: 0.1390 time to fit residues: 22.6188 Evaluate side-chains 112 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 60 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 155 MET 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 142 HIS 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 C residue 258 ILE Chi-restraints excluded: chain D residue 235 LYS 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 D residue 265 VAL 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 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 97 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 260 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 240 LEU 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 256 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 122 optimal weight: 20.0000 chunk 68 optimal weight: 0.7980 chunk 24 optimal weight: 8.9990 chunk 116 optimal weight: 20.0000 chunk 105 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 86 optimal weight: 0.0670 chunk 85 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 GLN ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.053383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.036939 restraints weight = 100780.415| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 5.18 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13080 Z= 0.141 Angle : 0.712 10.313 18429 Z= 0.390 Chirality : 0.047 0.298 2036 Planarity : 0.005 0.043 1774 Dihedral : 27.204 179.474 3030 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.03 % Favored : 82.97 % Rotamer: Outliers : 4.13 % Allowed : 33.88 % 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 are not related in a simple way. whole: -2.85 (0.24), residues: 1145 helix: 0.13 (0.30), residues: 316 sheet: -1.76 (0.34), residues: 197 loop : -3.17 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 227 TYR 0.017 0.001 TYR E 246 PHE 0.007 0.001 PHE A 199 TRP 0.047 0.001 TRP H 233 HIS 0.004 0.001 HIS A 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (13072) covalent geometry : angle 0.71185 / 0.39 (18426) hydrogen bonds : bond 0.04202 / 2.89 ( 460) hydrogen bonds : angle 4.40705 / 3.03 ( 1162) metal coordination : bond 0.01073 / 0.65 ( 8) metal coordination : angle 2.02861 / 1.64 ( 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 105 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 65 time to evaluate : 0.392 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: A 155 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7384 (mtt) REVERT: B 64 ASP cc_start: 0.8690 (t70) cc_final: 0.8276 (t70) REVERT: D 244 ARG cc_start: 0.8093 (mpt180) cc_final: 0.7884 (mpt180) REVERT: F 64 ASP cc_start: 0.7897 (t0) cc_final: 0.7447 (t0) REVERT: G 225 LYS cc_start: 0.9251 (mmmm) cc_final: 0.8821 (mmmm) outliers start: 40 outliers final: 33 residues processed: 101 average time/residue: 0.1316 time to fit residues: 18.3811 Evaluate side-chains 96 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 62 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 155 MET 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 C residue 225 LYS Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 265 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 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 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 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: 10.0000 chunk 101 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 251 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 = 0.3613 r_free = 0.3613 target = 0.052950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.036456 restraints weight = 101726.217| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 5.58 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13080 Z= 0.170 Angle : 0.713 10.578 18429 Z= 0.391 Chirality : 0.047 0.294 2036 Planarity : 0.005 0.045 1774 Dihedral : 27.214 179.690 3030 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.55 % Favored : 82.45 % Rotamer: Outliers : 4.65 % Allowed : 33.57 % Favored : 61.78 % 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 are not related in a simple way. whole: -2.92 (0.24), residues: 1145 helix: 0.09 (0.30), residues: 316 sheet: -1.83 (0.33), residues: 197 loop : -3.22 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 227 TYR 0.016 0.001 TYR E 246 PHE 0.010 0.001 PHE A 199 TRP 0.082 0.001 TRP H 233 HIS 0.005 0.001 HIS E 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.17 (13072) covalent geometry : angle 0.71235 / 0.39 (18426) hydrogen bonds : bond 0.04758 / 3.31 ( 460) hydrogen bonds : angle 4.42598 / 3.06 ( 1162) metal coordination : bond 0.00352 / 0.20 ( 8) metal coordination : angle 2.43509 / 1.75 ( 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 106 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 61 time to evaluate : 0.313 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: A 155 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7431 (mtt) REVERT: A 158 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8778 (tpt-90) REVERT: B 64 ASP cc_start: 0.8698 (t70) cc_final: 0.8254 (t70) REVERT: F 64 ASP cc_start: 0.8007 (t0) cc_final: 0.7513 (t0) REVERT: F 91 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8465 (p) REVERT: F 114 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7943 (ttt90) REVERT: F 266 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8653 (mmtm) REVERT: G 225 LYS cc_start: 0.9264 (mmmm) cc_final: 0.8823 (mmmm) outliers start: 45 outliers final: 37 residues processed: 100 average time/residue: 0.1361 time to fit residues: 18.6254 Evaluate side-chains 103 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 61 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 155 MET 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 C residue 225 LYS Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 265 VAL 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 91 THR Chi-restraints excluded: chain F residue 114 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 254 THR 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: 0.6980 chunk 23 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 122 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 251 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 = 0.3611 r_free = 0.3611 target = 0.052827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.036316 restraints weight = 101653.209| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 5.54 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13080 Z= 0.169 Angle : 0.723 10.995 18429 Z= 0.393 Chirality : 0.047 0.297 2036 Planarity : 0.005 0.042 1774 Dihedral : 27.254 179.136 3030 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.38 % Favored : 82.62 % Rotamer: Outliers : 4.86 % Allowed : 33.37 % Favored : 61.78 % 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 are not related in a simple way. whole: -2.92 (0.24), residues: 1145 helix: 0.10 (0.30), residues: 316 sheet: -1.84 (0.33), residues: 197 loop : -3.21 (0.22), residues: 632 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 0.051 0.001 TRP H 233 HIS 0.005 0.001 HIS E 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (13072) covalent geometry : angle 0.72248 / 0.39 (18426) hydrogen bonds : bond 0.04721 / 3.27 ( 460) hydrogen bonds : angle 4.41684 / 3.05 ( 1162) metal coordination : bond 0.00313 / 0.17 ( 8) metal coordination : angle 2.47158 / 1.83 ( 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 109 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 62 time to evaluate : 0.414 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: 0.7898 (OUTLIER) cc_final: 0.7448 (mtt) REVERT: A 158 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8762 (tpt-90) REVERT: B 64 ASP cc_start: 0.8747 (t70) cc_final: 0.8338 (t70) REVERT: F 64 ASP cc_start: 0.8019 (t0) cc_final: 0.7583 (t0) REVERT: F 91 THR cc_start: 0.8806 (OUTLIER) cc_final: 0.8461 (p) REVERT: F 266 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8634 (mmtm) REVERT: G 225 LYS cc_start: 0.9257 (mmmm) cc_final: 0.8838 (mmmm) outliers start: 47 outliers final: 38 residues processed: 104 average time/residue: 0.1407 time to fit residues: 19.9566 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 : 0.326 ------------------------------------------------------------------------------- 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 155 MET 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 C residue 225 LYS Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 265 VAL 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 91 THR 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 254 THR 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: 1.9990 chunk 105 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 19 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3612 r_free = 0.3612 target = 0.052884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.036393 restraints weight = 101118.537| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 5.48 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13080 Z= 0.161 Angle : 0.725 13.365 18429 Z= 0.393 Chirality : 0.047 0.298 2036 Planarity : 0.005 0.045 1774 Dihedral : 27.252 179.100 3030 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.29 % Favored : 82.71 % Rotamer: Outliers : 4.75 % Allowed : 33.16 % 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 are not related in a simple way. whole: -2.89 (0.24), residues: 1145 helix: 0.12 (0.30), residues: 316 sheet: -1.83 (0.34), residues: 197 loop : -3.19 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 244 TYR 0.016 0.001 TYR E 246 PHE 0.009 0.001 PHE A 199 TRP 0.039 0.001 TRP H 233 HIS 0.005 0.001 HIS E 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (13072) covalent geometry : angle 0.72402 / 0.39 (18426) hydrogen bonds : bond 0.04565 / 3.16 ( 460) hydrogen bonds : angle 4.38642 / 3.04 ( 1162) metal coordination : bond 0.00396 / 0.23 ( 8) metal coordination : angle 2.38885 / 1.77 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2694.73 seconds wall clock time: 47 minutes 15.63 seconds (2835.63 seconds total)