Starting phenix.real_space_refine on Wed Jul 30 13:40:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e14_27823/07_2025/8e14_27823.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e14_27823/07_2025/8e14_27823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e14_27823/07_2025/8e14_27823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e14_27823/07_2025/8e14_27823.map" model { file = "/net/cci-nas-00/data/ceres_data/8e14_27823/07_2025/8e14_27823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e14_27823/07_2025/8e14_27823.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 9.02, per 1000 atoms: 0.72 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: 3.41 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 5.23 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: 4.91 Time building geometry restraints manager: 4.02 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: 124.790 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 39.770 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 168.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.280 13080 Z= 0.346 Angle : 1.125 61.523 18429 Z= 0.580 Chirality : 0.083 3.078 2036 Planarity : 0.006 0.152 1774 Dihedral : 24.724 179.828 5263 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 16.48 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.127 0.001 TRP H 233 HIS 0.006 0.001 HIS B 93 PHE 0.005 0.001 PHE A 199 TYR 0.017 0.001 TYR E 246 ARG 0.034 0.001 ARG H 244 Details of bonding type rmsd hydrogen bonds : bond 0.07794 ( 460) hydrogen bonds : angle 4.22499 ( 1162) metal coordination : bond 0.00371 ( 8) metal coordination : angle 3.28923 ( 3) covalent geometry : bond 0.00689 (13072) covalent geometry : angle 1.12410 (18426) *********************** 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 : 1.230 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: 0.3387 time to fit residues: 28.1406 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 : 1.667 ------------------------------------------------------------------------------- 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 104 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.052563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.036315 restraints weight = 101373.758| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 4.86 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 13080 Z= 0.233 Angle : 0.692 9.091 18429 Z= 0.381 Chirality : 0.043 0.213 2036 Planarity : 0.005 0.077 1774 Dihedral : 27.052 176.572 3033 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.08 % Favored : 81.92 % Rotamer: Outliers : 4.96 % Allowed : 32.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.23), residues: 1145 helix: 0.03 (0.30), residues: 302 sheet: -1.81 (0.35), residues: 186 loop : -3.22 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 233 HIS 0.006 0.001 HIS E 9 PHE 0.011 0.001 PHE A 199 TYR 0.019 0.001 TYR E 246 ARG 0.005 0.000 ARG D 244 Details of bonding type rmsd hydrogen bonds : bond 0.05559 ( 460) hydrogen bonds : angle 4.36846 ( 1162) metal coordination : bond 0.00552 ( 8) metal coordination : angle 3.26572 ( 3) covalent geometry : bond 0.00518 (13072) covalent geometry : angle 0.69114 (18426) *********************** 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 110 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 62 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8583 (mm) REVERT: B 64 ASP cc_start: 0.8618 (t0) cc_final: 0.8207 (t0) REVERT: D 244 ARG cc_start: 0.8257 (mpt180) cc_final: 0.8032 (mpt180) REVERT: E 193 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7534 (mpt) REVERT: F 64 ASP cc_start: 0.7937 (t0) cc_final: 0.7669 (t0) REVERT: G 225 LYS cc_start: 0.9246 (mmmm) cc_final: 0.8864 (mmmm) REVERT: H 233 TRP cc_start: 0.8771 (m100) cc_final: 0.8544 (m100) outliers start: 48 outliers final: 26 residues processed: 103 average time/residue: 0.3040 time to fit residues: 43.9064 Evaluate side-chains 87 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 59 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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 265 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain D residue 228 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 193 MET Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 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 86 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 95 optimal weight: 0.1980 chunk 2 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 chunk 40 optimal weight: 0.0030 chunk 69 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.053554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.037002 restraints weight = 101560.397| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 5.43 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13080 Z= 0.149 Angle : 0.645 10.049 18429 Z= 0.354 Chirality : 0.041 0.214 2036 Planarity : 0.005 0.060 1774 Dihedral : 26.941 179.983 3030 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.77 % Favored : 83.23 % Rotamer: Outliers : 5.17 % Allowed : 31.51 % Favored : 63.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.24), residues: 1145 helix: 0.25 (0.31), residues: 302 sheet: -1.33 (0.36), residues: 173 loop : -3.16 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 237 HIS 0.005 0.001 HIS B 93 PHE 0.007 0.001 PHE A 199 TYR 0.016 0.001 TYR E 246 ARG 0.004 0.000 ARG C 227 Details of bonding type rmsd hydrogen bonds : bond 0.03745 ( 460) hydrogen bonds : angle 4.14360 ( 1162) metal coordination : bond 0.00767 ( 8) metal coordination : angle 2.70077 ( 3) covalent geometry : bond 0.00332 (13072) covalent geometry : angle 0.64429 (18426) *********************** 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 116 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 66 time to evaluate : 1.222 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: 0.8471 (t0) cc_final: 0.8106 (t70) REVERT: F 64 ASP cc_start: 0.7930 (t0) cc_final: 0.7473 (t0) REVERT: G 225 LYS cc_start: 0.9246 (mmmm) cc_final: 0.8686 (mmmm) REVERT: H 227 ARG cc_start: 0.7751 (mtt90) cc_final: 0.7386 (mmm160) REVERT: H 233 TRP cc_start: 0.9001 (m100) cc_final: 0.8618 (m100) outliers start: 50 outliers final: 26 residues processed: 112 average time/residue: 0.2903 time to fit residues: 44.9949 Evaluate side-chains 87 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 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 E residue 35 GLN Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 103 HIS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 238 ASN Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 268 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 16 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.052862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.036576 restraints weight = 101252.583| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 4.83 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13080 Z= 0.195 Angle : 0.670 10.258 18429 Z= 0.366 Chirality : 0.042 0.257 2036 Planarity : 0.005 0.057 1774 Dihedral : 26.970 176.513 3030 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.03 % Favored : 82.97 % Rotamer: Outliers : 5.79 % Allowed : 32.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.24), residues: 1145 helix: 0.17 (0.30), residues: 304 sheet: -1.78 (0.34), residues: 190 loop : -3.14 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 237 HIS 0.005 0.001 HIS E 9 PHE 0.009 0.001 PHE A 199 TYR 0.018 0.001 TYR E 246 ARG 0.006 0.000 ARG D 244 Details of bonding type rmsd hydrogen bonds : bond 0.04885 ( 460) hydrogen bonds : angle 4.25344 ( 1162) metal coordination : bond 0.00249 ( 8) metal coordination : angle 2.65638 ( 3) covalent geometry : bond 0.00434 (13072) covalent geometry : angle 0.66900 (18426) *********************** 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 117 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 61 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 ASP cc_start: 0.8602 (t0) cc_final: 0.8221 (t70) REVERT: F 64 ASP cc_start: 0.7871 (t0) cc_final: 0.7400 (t0) REVERT: F 114 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8584 (ttm-80) REVERT: G 225 LYS cc_start: 0.9253 (mmmm) cc_final: 0.8829 (mmmm) REVERT: H 227 ARG cc_start: 0.7986 (mtt90) cc_final: 0.7172 (mmm160) outliers start: 56 outliers final: 35 residues processed: 110 average time/residue: 0.3012 time to fit residues: 45.5901 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 : 1.298 ------------------------------------------------------------------------------- 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 224 VAL Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 103 HIS Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 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 254 THR Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 268 ASP Chi-restraints excluded: chain H residue 256 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 96 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.052828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.036277 restraints weight = 101591.379| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 5.41 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13080 Z= 0.193 Angle : 0.672 9.549 18429 Z= 0.367 Chirality : 0.042 0.225 2036 Planarity : 0.005 0.052 1774 Dihedral : 26.986 176.637 3030 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.38 % Favored : 82.62 % Rotamer: Outliers : 6.40 % Allowed : 31.71 % Favored : 61.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.24), residues: 1145 helix: 0.07 (0.30), residues: 316 sheet: -1.80 (0.34), residues: 190 loop : -3.16 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 237 HIS 0.005 0.001 HIS E 9 PHE 0.010 0.001 PHE A 199 TYR 0.017 0.001 TYR E 246 ARG 0.005 0.000 ARG D 244 Details of bonding type rmsd hydrogen bonds : bond 0.04656 ( 460) hydrogen bonds : angle 4.25327 ( 1162) metal coordination : bond 0.00263 ( 8) metal coordination : angle 2.53611 ( 3) covalent geometry : bond 0.00429 (13072) covalent geometry : angle 0.67167 (18426) *********************** 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 123 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 61 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8192 (mtp180) REVERT: A 158 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8771 (tpt-90) REVERT: B 64 ASP cc_start: 0.8631 (t0) cc_final: 0.8216 (t70) REVERT: F 64 ASP cc_start: 0.7860 (t0) cc_final: 0.7428 (t0) REVERT: F 114 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8582 (ttm-80) REVERT: F 266 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8682 (mmtm) REVERT: G 225 LYS cc_start: 0.9284 (mmmm) cc_final: 0.8870 (mmmm) outliers start: 62 outliers final: 41 residues processed: 115 average time/residue: 0.3047 time to fit residues: 47.5209 Evaluate side-chains 101 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 56 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 226 ILE 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 E residue 35 GLN Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 103 HIS Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 178 LYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 161 ARG Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 238 ASN Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain 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 254 THR Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 268 ASP Chi-restraints excluded: chain H residue 256 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 18 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 67 optimal weight: 0.0770 chunk 70 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.053334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.036809 restraints weight = 101324.304| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 5.24 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1389 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= 0.154 Angle : 0.666 9.568 18429 Z= 0.362 Chirality : 0.042 0.214 2036 Planarity : 0.005 0.050 1774 Dihedral : 26.937 177.723 3030 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.94 % Favored : 83.06 % Rotamer: Outliers : 5.06 % Allowed : 32.75 % Favored : 62.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.24), residues: 1145 helix: 0.20 (0.30), residues: 316 sheet: -1.62 (0.34), residues: 192 loop : -3.16 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 237 HIS 0.004 0.001 HIS E 9 PHE 0.007 0.001 PHE A 199 TYR 0.016 0.001 TYR E 246 ARG 0.004 0.000 ARG D 244 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 460) hydrogen bonds : angle 4.23683 ( 1162) metal coordination : bond 0.00667 ( 8) metal coordination : angle 2.48357 ( 3) covalent geometry : bond 0.00346 (13072) covalent geometry : angle 0.66553 (18426) *********************** 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: 49 poor density : 65 time to evaluate : 1.368 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: 0.7696 (mtt) cc_final: 0.7352 (mtt) REVERT: A 158 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8747 (tpt-90) REVERT: B 64 ASP cc_start: 0.8756 (t70) cc_final: 0.8343 (t70) REVERT: F 64 ASP cc_start: 0.7896 (t0) cc_final: 0.7439 (t0) REVERT: F 114 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8590 (ttm-80) REVERT: G 225 LYS cc_start: 0.9256 (mmmm) cc_final: 0.8826 (mmmm) outliers start: 49 outliers final: 38 residues processed: 109 average time/residue: 0.3252 time to fit residues: 48.3501 Evaluate side-chains 97 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 57 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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 158 ARG 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 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 170 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 161 ARG Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 238 ASN Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 268 ASP Chi-restraints excluded: chain H residue 256 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 92 optimal weight: 0.6980 chunk 84 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN E 238 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.052664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.036137 restraints weight = 101746.860| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 5.51 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13080 Z= 0.205 Angle : 0.694 9.178 18429 Z= 0.376 Chirality : 0.042 0.214 2036 Planarity : 0.005 0.047 1774 Dihedral : 26.988 175.946 3030 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.17 % Favored : 81.83 % Rotamer: Outliers : 6.40 % Allowed : 31.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.24), residues: 1145 helix: 0.09 (0.30), residues: 316 sheet: -1.79 (0.34), residues: 189 loop : -3.14 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 237 HIS 0.005 0.001 HIS E 9 PHE 0.010 0.001 PHE A 199 TYR 0.017 0.001 TYR E 246 ARG 0.004 0.000 ARG C 227 Details of bonding type rmsd hydrogen bonds : bond 0.04887 ( 460) hydrogen bonds : angle 4.33503 ( 1162) metal coordination : bond 0.00337 ( 8) metal coordination : angle 2.66339 ( 3) covalent geometry : bond 0.00459 (13072) covalent geometry : angle 0.69318 (18426) *********************** 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 123 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 61 time to evaluate : 1.523 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 158 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8773 (tpt-90) REVERT: B 64 ASP cc_start: 0.8715 (t70) cc_final: 0.8266 (t70) REVERT: E 193 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7310 (mpt) REVERT: F 64 ASP cc_start: 0.8057 (t0) cc_final: 0.7618 (t0) REVERT: F 91 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8441 (p) REVERT: F 114 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8577 (ttm-80) REVERT: F 266 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8684 (mmtm) REVERT: G 225 LYS cc_start: 0.9300 (mmmm) cc_final: 0.8868 (mmmm) REVERT: G 256 LYS cc_start: 0.8909 (mtmm) cc_final: 0.8395 (mtmm) outliers start: 62 outliers final: 46 residues processed: 116 average time/residue: 0.3259 time to fit residues: 51.9366 Evaluate side-chains 109 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 58 time to evaluate : 1.398 ------------------------------------------------------------------------------- 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 124 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 146 ILE 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 249 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain C residue 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 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 170 LEU Chi-restraints excluded: chain E residue 178 LYS Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 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 91 THR Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 161 ARG Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 238 ASN Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 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 254 THR Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 268 ASP Chi-restraints excluded: chain H residue 256 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.053067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.036527 restraints weight = 101720.982| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 5.80 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13080 Z= 0.165 Angle : 0.680 9.709 18429 Z= 0.367 Chirality : 0.042 0.215 2036 Planarity : 0.005 0.046 1774 Dihedral : 26.981 177.099 3030 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.77 % Favored : 83.23 % Rotamer: Outliers : 5.58 % Allowed : 32.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.24), residues: 1145 helix: 0.16 (0.30), residues: 316 sheet: -1.76 (0.34), residues: 189 loop : -3.09 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 237 HIS 0.004 0.001 HIS E 9 PHE 0.008 0.001 PHE A 199 TYR 0.016 0.001 TYR E 246 ARG 0.005 0.000 ARG C 227 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 460) hydrogen bonds : angle 4.26831 ( 1162) metal coordination : bond 0.00426 ( 8) metal coordination : angle 2.41510 ( 3) covalent geometry : bond 0.00370 (13072) covalent geometry : angle 0.67943 (18426) *********************** 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 116 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 62 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8748 (tpt-90) REVERT: B 64 ASP cc_start: 0.8734 (t70) cc_final: 0.8266 (t70) REVERT: F 64 ASP cc_start: 0.8097 (t0) cc_final: 0.7740 (t0) REVERT: G 225 LYS cc_start: 0.9309 (mmmm) cc_final: 0.8912 (mmmm) REVERT: G 256 LYS cc_start: 0.8883 (mtmm) cc_final: 0.8638 (mtmm) outliers start: 54 outliers final: 43 residues processed: 111 average time/residue: 0.2959 time to fit residues: 45.4951 Evaluate side-chains 105 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 61 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 65 PHE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 103 HIS Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 161 ARG Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 238 ASN Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 265 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 65 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.052805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.036415 restraints weight = 102017.139| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 5.64 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13080 Z= 0.184 Angle : 0.694 11.209 18429 Z= 0.374 Chirality : 0.042 0.214 2036 Planarity : 0.005 0.045 1774 Dihedral : 26.994 176.259 3030 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.47 % Favored : 82.53 % Rotamer: Outliers : 5.68 % Allowed : 31.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.24), residues: 1145 helix: 0.12 (0.30), residues: 316 sheet: -1.78 (0.34), residues: 189 loop : -3.12 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 237 HIS 0.004 0.001 HIS E 9 PHE 0.009 0.001 PHE A 199 TYR 0.017 0.001 TYR E 246 ARG 0.004 0.000 ARG C 227 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 460) hydrogen bonds : angle 4.30054 ( 1162) metal coordination : bond 0.00272 ( 8) metal coordination : angle 2.54695 ( 3) covalent geometry : bond 0.00413 (13072) covalent geometry : angle 0.69283 (18426) *********************** 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 115 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 60 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8776 (tpt-90) REVERT: B 64 ASP cc_start: 0.8795 (t70) cc_final: 0.8328 (t70) REVERT: F 64 ASP cc_start: 0.8241 (t0) cc_final: 0.7858 (t0) REVERT: F 91 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8405 (p) REVERT: F 114 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7970 (ttt90) REVERT: G 225 LYS cc_start: 0.9314 (mmmm) cc_final: 0.8899 (mmmm) REVERT: G 256 LYS cc_start: 0.8917 (mtmm) cc_final: 0.8666 (mtmm) outliers start: 55 outliers final: 45 residues processed: 110 average time/residue: 0.3074 time to fit residues: 46.1877 Evaluate side-chains 108 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 60 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 65 PHE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 103 HIS Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 170 LEU 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 91 THR Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 161 ARG Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 238 ASN Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 268 ASP Chi-restraints excluded: chain H residue 256 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 46 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 66 optimal weight: 0.1980 chunk 109 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN F 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.053467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.036990 restraints weight = 100926.160| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 5.75 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13080 Z= 0.149 Angle : 0.695 12.056 18429 Z= 0.372 Chirality : 0.042 0.214 2036 Planarity : 0.005 0.046 1774 Dihedral : 26.937 177.837 3030 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.86 % Favored : 83.14 % Rotamer: Outliers : 4.55 % Allowed : 32.85 % Favored : 62.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.24), residues: 1145 helix: 0.14 (0.30), residues: 320 sheet: -1.42 (0.36), residues: 177 loop : -3.03 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 237 HIS 0.004 0.001 HIS A 13 PHE 0.005 0.001 PHE A 199 TYR 0.015 0.001 TYR E 246 ARG 0.016 0.000 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.03487 ( 460) hydrogen bonds : angle 4.19266 ( 1162) metal coordination : bond 0.00743 ( 8) metal coordination : angle 2.83545 ( 3) covalent geometry : bond 0.00336 (13072) covalent geometry : angle 0.69401 (18426) ********************** 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: 44 poor density : 65 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8715 (tpt-90) REVERT: B 64 ASP cc_start: 0.8790 (t70) cc_final: 0.8382 (t70) REVERT: E 64 ASP cc_start: 0.8653 (t0) cc_final: 0.8340 (t0) REVERT: F 64 ASP cc_start: 0.8169 (t0) cc_final: 0.7821 (t0) REVERT: F 91 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8442 (p) REVERT: F 114 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8526 (ttt90) REVERT: G 225 LYS cc_start: 0.9296 (mmmm) cc_final: 0.8892 (mmmm) REVERT: G 256 LYS cc_start: 0.8865 (mtmm) cc_final: 0.8622 (mtmm) outliers start: 44 outliers final: 40 residues processed: 108 average time/residue: 0.3007 time to fit residues: 44.4513 Evaluate side-chains 106 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 63 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 65 PHE Chi-restraints excluded: chain A residue 91 THR 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 158 ARG Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 65 PHE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 103 HIS Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 161 ARG Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 238 ASN Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain G residue 239 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 27 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 72 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.053201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.036756 restraints weight = 101001.681| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 5.16 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13080 Z= 0.166 Angle : 0.694 11.237 18429 Z= 0.372 Chirality : 0.042 0.210 2036 Planarity : 0.005 0.056 1774 Dihedral : 26.942 176.884 3030 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.94 % Favored : 83.06 % Rotamer: Outliers : 5.17 % Allowed : 32.23 % Favored : 62.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.24), residues: 1145 helix: 0.19 (0.30), residues: 316 sheet: -1.41 (0.36), residues: 167 loop : -3.03 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 237 HIS 0.004 0.001 HIS E 9 PHE 0.007 0.001 PHE A 199 TYR 0.016 0.001 TYR E 246 ARG 0.014 0.000 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 460) hydrogen bonds : angle 4.19394 ( 1162) metal coordination : bond 0.00399 ( 8) metal coordination : angle 2.94678 ( 3) covalent geometry : bond 0.00375 (13072) covalent geometry : angle 0.69348 (18426) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5954.58 seconds wall clock time: 104 minutes 29.75 seconds (6269.75 seconds total)