Starting phenix.real_space_refine on Fri Aug 22 23:44:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u4p_41890/08_2025/8u4p_41890.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4p_41890/08_2025/8u4p_41890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u4p_41890/08_2025/8u4p_41890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4p_41890/08_2025/8u4p_41890.map" model { file = "/net/cci-nas-00/data/ceres_data/8u4p_41890/08_2025/8u4p_41890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4p_41890/08_2025/8u4p_41890.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2008 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 4508 2.51 5 N 1179 2.21 5 O 1271 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7006 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1777 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2516 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 4, 'GLU:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 345 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 2304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2304 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain: "R" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'CLR': 1, 'VH6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.82, per 1000 atoms: 0.26 Number of scatterers: 7006 At special positions: 0 Unit cell: (73.1, 102, 130.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1271 8.00 N 1179 7.00 C 4508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 186 " distance=2.03 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: 0.46 Conformation dependent library (CDL) restraints added in 385.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1690 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 9 sheets defined 45.9% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.662A pdb=" N LYS A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.652A pdb=" N LYS A 51 " --> pdb=" O CYS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.501A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.526A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.641A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'R' and resid 34 through 65 Proline residue: R 42 - end of helix Processing helix chain 'R' and resid 73 through 90 Processing helix chain 'R' and resid 90 through 100 removed outlier: 4.186A pdb=" N TRP R 94 " --> pdb=" O THR R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 140 removed outlier: 3.789A pdb=" N VAL R 124 " --> pdb=" O LEU R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 167 removed outlier: 3.613A pdb=" N LYS R 149 " --> pdb=" O GLN R 145 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TYR R 157 " --> pdb=" O GLU R 153 " (cutoff:3.500A) Proline residue: R 163 - end of helix Processing helix chain 'R' and resid 168 through 174 Processing helix chain 'R' and resid 192 through 208 removed outlier: 3.682A pdb=" N VAL R 196 " --> pdb=" O ASN R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 227 removed outlier: 3.669A pdb=" N LYS R 225 " --> pdb=" O ILE R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 267 removed outlier: 3.863A pdb=" N ALA R 237 " --> pdb=" O GLN R 233 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU R 238 " --> pdb=" O LYS R 234 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE R 243 " --> pdb=" O LYS R 239 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU R 244 " --> pdb=" O THR R 240 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU R 246 " --> pdb=" O VAL R 242 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N CYS R 251 " --> pdb=" O ALA R 247 " (cutoff:3.500A) Proline residue: R 254 - end of helix Processing helix chain 'R' and resid 273 through 292 removed outlier: 3.670A pdb=" N GLU R 277 " --> pdb=" O GLY R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 303 Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 306 through 318 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.584A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.843A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.822A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.076A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.595A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.676A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.620A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.835A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 175 through 180 removed outlier: 3.597A pdb=" N ASN R 176 " --> pdb=" O ASP R 187 " (cutoff:3.500A) 365 hydrogen bonds defined for protein. 1062 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2220 1.34 - 1.46: 1251 1.46 - 1.57: 3618 1.57 - 1.69: 4 1.69 - 1.81: 65 Bond restraints: 7158 Sorted by residual: bond pdb=" C22 VH6 R 702 " pdb=" N23 VH6 R 702 " ideal model delta sigma weight residual 1.446 1.535 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C24 VH6 R 702 " pdb=" N23 VH6 R 702 " ideal model delta sigma weight residual 1.457 1.527 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C36 VH6 R 702 " pdb=" N23 VH6 R 702 " ideal model delta sigma weight residual 1.455 1.520 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C07 VH6 R 702 " pdb=" N08 VH6 R 702 " ideal model delta sigma weight residual 1.455 1.513 -0.058 2.00e-02 2.50e+03 8.35e+00 bond pdb=" C15 VH6 R 702 " pdb=" N08 VH6 R 702 " ideal model delta sigma weight residual 1.456 1.513 -0.057 2.00e-02 2.50e+03 8.10e+00 ... (remaining 7153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 9518 1.57 - 3.14: 149 3.14 - 4.71: 25 4.71 - 6.28: 12 6.28 - 7.84: 3 Bond angle restraints: 9707 Sorted by residual: angle pdb=" C22 CLR R 701 " pdb=" C23 CLR R 701 " pdb=" C24 CLR R 701 " ideal model delta sigma weight residual 111.95 104.11 7.84 3.00e+00 1.11e-01 6.84e+00 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 121.54 126.39 -4.85 1.91e+00 2.74e-01 6.45e+00 angle pdb=" C24 VH6 R 702 " pdb=" N23 VH6 R 702 " pdb=" C36 VH6 R 702 " ideal model delta sigma weight residual 115.20 107.60 7.60 3.00e+00 1.11e-01 6.42e+00 angle pdb=" N LEU R 91 " pdb=" CA LEU R 91 " pdb=" C LEU R 91 " ideal model delta sigma weight residual 109.81 115.19 -5.38 2.21e+00 2.05e-01 5.94e+00 angle pdb=" C GLY R 159 " pdb=" N VAL R 160 " pdb=" CA VAL R 160 " ideal model delta sigma weight residual 122.35 119.56 2.79 1.18e+00 7.18e-01 5.57e+00 ... (remaining 9702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 3860 17.81 - 35.61: 358 35.61 - 53.42: 64 53.42 - 71.23: 5 71.23 - 89.03: 9 Dihedral angle restraints: 4296 sinusoidal: 1690 harmonic: 2606 Sorted by residual: dihedral pdb=" CB GLU B 260 " pdb=" CG GLU B 260 " pdb=" CD GLU B 260 " pdb=" OE1 GLU B 260 " ideal model delta sinusoidal sigma weight residual 0.00 89.03 -89.03 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU A 276 " pdb=" CG GLU A 276 " pdb=" CD GLU A 276 " pdb=" OE1 GLU A 276 " ideal model delta sinusoidal sigma weight residual 0.00 87.27 -87.27 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CG ARG B 22 " pdb=" CD ARG B 22 " pdb=" NE ARG B 22 " pdb=" CZ ARG B 22 " ideal model delta sinusoidal sigma weight residual -180.00 -136.41 -43.59 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 4293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1016 0.071 - 0.142: 99 0.142 - 0.212: 0 0.212 - 0.283: 1 0.283 - 0.354: 3 Chirality restraints: 1119 Sorted by residual: chirality pdb=" C17 CLR R 701 " pdb=" C13 CLR R 701 " pdb=" C16 CLR R 701 " pdb=" C20 CLR R 701 " both_signs ideal model delta sigma weight residual False 2.55 2.91 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" C20 CLR R 701 " pdb=" C17 CLR R 701 " pdb=" C21 CLR R 701 " pdb=" C22 CLR R 701 " both_signs ideal model delta sigma weight residual False 2.59 2.90 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C13 CLR R 701 " pdb=" C12 CLR R 701 " pdb=" C14 CLR R 701 " pdb=" C17 CLR R 701 " both_signs ideal model delta sigma weight residual False -2.93 -3.23 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 1116 not shown) Planarity restraints: 1208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA R 152 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.28e+00 pdb=" C ALA R 152 " 0.047 2.00e-02 2.50e+03 pdb=" O ALA R 152 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU R 153 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 298 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO R 299 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO R 299 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 299 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 158 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.02e+00 pdb=" C VAL R 158 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL R 158 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY R 159 " 0.008 2.00e-02 2.50e+03 ... (remaining 1205 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1206 2.77 - 3.30: 6419 3.30 - 3.84: 10965 3.84 - 4.37: 12820 4.37 - 4.90: 23460 Nonbonded interactions: 54870 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.240 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.245 3.040 nonbonded pdb=" OG SER A 293 " pdb=" OE1 GLU A 298 " model vdw 2.281 3.040 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.313 3.120 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.315 3.120 ... (remaining 54865 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.720 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 7159 Z= 0.176 Angle : 0.530 7.844 9709 Z= 0.265 Chirality : 0.044 0.354 1119 Planarity : 0.003 0.036 1208 Dihedral : 14.369 89.035 2603 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.29), residues: 882 helix: 1.74 (0.28), residues: 381 sheet: -0.17 (0.38), residues: 180 loop : -1.02 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 70 TYR 0.008 0.001 TYR R 116 PHE 0.012 0.001 PHE A 189 TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS R 79 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 7158) covalent geometry : angle 0.53019 ( 9707) SS BOND : bond 0.00143 ( 1) SS BOND : angle 1.06287 ( 2) hydrogen bonds : bond 0.15820 ( 365) hydrogen bonds : angle 5.94274 ( 1062) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.272 Fit side-chains REVERT: A 53 MET cc_start: 0.3392 (ttt) cc_final: 0.3192 (ttp) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0985 time to fit residues: 12.0850 Evaluate side-chains 75 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** 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 = 0.3581 r_free = 0.3581 target = 0.143269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.101606 restraints weight = 7990.777| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.32 r_work: 0.2865 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7159 Z= 0.141 Angle : 0.498 5.980 9709 Z= 0.270 Chirality : 0.041 0.137 1119 Planarity : 0.004 0.036 1208 Dihedral : 4.861 30.455 1057 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.21 % Allowed : 5.94 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.29), residues: 882 helix: 2.03 (0.28), residues: 382 sheet: -0.14 (0.38), residues: 182 loop : -0.86 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 70 TYR 0.011 0.001 TYR B 59 PHE 0.014 0.001 PHE A 189 TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS R 79 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7158) covalent geometry : angle 0.49798 ( 9707) SS BOND : bond 0.00054 ( 1) SS BOND : angle 1.59535 ( 2) hydrogen bonds : bond 0.05231 ( 365) hydrogen bonds : angle 4.69445 ( 1062) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.291 Fit side-chains REVERT: A 10 LYS cc_start: 0.7039 (tptt) cc_final: 0.6748 (tppt) REVERT: B 290 ASP cc_start: 0.8611 (m-30) cc_final: 0.8330 (m-30) outliers start: 9 outliers final: 8 residues processed: 93 average time/residue: 0.1059 time to fit residues: 12.7013 Evaluate side-chains 84 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain R residue 131 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 81 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** 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 = 0.3636 r_free = 0.3636 target = 0.147146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.106989 restraints weight = 7835.114| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.28 r_work: 0.3000 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7159 Z= 0.120 Angle : 0.471 5.857 9709 Z= 0.255 Chirality : 0.040 0.135 1119 Planarity : 0.003 0.036 1208 Dihedral : 4.627 29.450 1057 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.62 % Allowed : 7.02 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.29), residues: 882 helix: 2.19 (0.28), residues: 382 sheet: -0.09 (0.38), residues: 181 loop : -0.83 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 219 TYR 0.008 0.001 TYR B 59 PHE 0.014 0.001 PHE A 189 TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS R 79 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7158) covalent geometry : angle 0.47093 ( 9707) SS BOND : bond 0.00051 ( 1) SS BOND : angle 1.27531 ( 2) hydrogen bonds : bond 0.04631 ( 365) hydrogen bonds : angle 4.48143 ( 1062) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.219 Fit side-chains REVERT: A 10 LYS cc_start: 0.6967 (tptt) cc_final: 0.6668 (tppt) REVERT: B 290 ASP cc_start: 0.8570 (m-30) cc_final: 0.8287 (m-30) outliers start: 12 outliers final: 9 residues processed: 87 average time/residue: 0.0926 time to fit residues: 10.4775 Evaluate side-chains 83 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 131 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 26 optimal weight: 0.2980 chunk 7 optimal weight: 0.1980 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 48 optimal weight: 0.0270 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 0.1980 chunk 54 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 overall best weight: 0.1838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.152224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.111485 restraints weight = 7830.600| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.30 r_work: 0.2963 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7159 Z= 0.087 Angle : 0.425 5.671 9709 Z= 0.231 Chirality : 0.039 0.142 1119 Planarity : 0.003 0.035 1208 Dihedral : 4.262 28.771 1057 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.54 % Allowed : 9.85 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.29), residues: 882 helix: 2.33 (0.28), residues: 383 sheet: 0.13 (0.38), residues: 184 loop : -0.66 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 70 TYR 0.006 0.001 TYR R 116 PHE 0.011 0.001 PHE A 189 TRP 0.010 0.001 TRP B 82 HIS 0.002 0.000 HIS R 79 Details of bonding type rmsd covalent geometry : bond 0.00167 ( 7158) covalent geometry : angle 0.42489 ( 9707) SS BOND : bond 0.00040 ( 1) SS BOND : angle 0.61022 ( 2) hydrogen bonds : bond 0.03517 ( 365) hydrogen bonds : angle 4.22858 ( 1062) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.173 Fit side-chains REVERT: B 154 ASP cc_start: 0.9013 (OUTLIER) cc_final: 0.8740 (t0) REVERT: B 290 ASP cc_start: 0.8559 (m-30) cc_final: 0.8261 (m-30) outliers start: 4 outliers final: 2 residues processed: 89 average time/residue: 0.1036 time to fit residues: 11.8365 Evaluate side-chains 77 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain R residue 131 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 37 optimal weight: 0.8980 chunk 10 optimal weight: 0.0770 chunk 34 optimal weight: 0.0570 chunk 6 optimal weight: 0.0170 chunk 65 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 overall best weight: 0.3694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.150796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.109742 restraints weight = 7841.994| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.31 r_work: 0.2926 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7159 Z= 0.093 Angle : 0.440 5.574 9709 Z= 0.239 Chirality : 0.039 0.157 1119 Planarity : 0.003 0.038 1208 Dihedral : 4.197 27.256 1057 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.21 % Allowed : 9.85 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.29), residues: 882 helix: 2.44 (0.28), residues: 384 sheet: 0.19 (0.38), residues: 184 loop : -0.63 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.008 0.001 TYR B 59 PHE 0.012 0.001 PHE A 189 TRP 0.009 0.001 TRP B 82 HIS 0.002 0.000 HIS R 79 Details of bonding type rmsd covalent geometry : bond 0.00191 ( 7158) covalent geometry : angle 0.43994 ( 9707) SS BOND : bond 0.00007 ( 1) SS BOND : angle 0.67223 ( 2) hydrogen bonds : bond 0.03650 ( 365) hydrogen bonds : angle 4.17353 ( 1062) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.229 Fit side-chains REVERT: B 154 ASP cc_start: 0.9011 (OUTLIER) cc_final: 0.8743 (t0) REVERT: B 290 ASP cc_start: 0.8509 (m-30) cc_final: 0.8197 (m-30) outliers start: 9 outliers final: 6 residues processed: 87 average time/residue: 0.0994 time to fit residues: 11.1289 Evaluate side-chains 80 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 131 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 0.0060 chunk 66 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 75 optimal weight: 30.0000 chunk 83 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.146415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.104341 restraints weight = 7874.577| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.35 r_work: 0.2860 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7159 Z= 0.111 Angle : 0.460 5.657 9709 Z= 0.247 Chirality : 0.040 0.139 1119 Planarity : 0.003 0.037 1208 Dihedral : 4.343 26.819 1057 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.62 % Allowed : 10.66 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.29), residues: 882 helix: 2.41 (0.28), residues: 384 sheet: 0.13 (0.38), residues: 184 loop : -0.65 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.007 0.001 TYR R 116 PHE 0.014 0.001 PHE A 189 TRP 0.008 0.001 TRP B 82 HIS 0.004 0.001 HIS R 79 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 7158) covalent geometry : angle 0.45995 ( 9707) SS BOND : bond 0.00016 ( 1) SS BOND : angle 0.95146 ( 2) hydrogen bonds : bond 0.04151 ( 365) hydrogen bonds : angle 4.23601 ( 1062) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.275 Fit side-chains REVERT: A 10 LYS cc_start: 0.7002 (tptt) cc_final: 0.6696 (tppt) REVERT: B 154 ASP cc_start: 0.9008 (OUTLIER) cc_final: 0.8755 (t0) REVERT: B 290 ASP cc_start: 0.8573 (m-30) cc_final: 0.8265 (m-30) outliers start: 12 outliers final: 9 residues processed: 88 average time/residue: 0.1115 time to fit residues: 12.5378 Evaluate side-chains 83 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 131 SER Chi-restraints excluded: chain R residue 186 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.148836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.110414 restraints weight = 7783.964| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.21 r_work: 0.2902 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7159 Z= 0.124 Angle : 0.475 5.821 9709 Z= 0.256 Chirality : 0.041 0.139 1119 Planarity : 0.003 0.037 1208 Dihedral : 4.485 27.083 1057 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.62 % Allowed : 11.20 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.29), residues: 882 helix: 2.37 (0.28), residues: 384 sheet: 0.06 (0.38), residues: 179 loop : -0.68 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.007 0.001 TYR A 320 PHE 0.014 0.001 PHE A 189 TRP 0.009 0.001 TRP B 63 HIS 0.005 0.001 HIS R 79 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 7158) covalent geometry : angle 0.47450 ( 9707) SS BOND : bond 0.00065 ( 1) SS BOND : angle 1.09848 ( 2) hydrogen bonds : bond 0.04461 ( 365) hydrogen bonds : angle 4.30320 ( 1062) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.287 Fit side-chains REVERT: A 10 LYS cc_start: 0.7100 (tptt) cc_final: 0.6758 (tppt) REVERT: B 154 ASP cc_start: 0.9017 (OUTLIER) cc_final: 0.8774 (t0) REVERT: B 290 ASP cc_start: 0.8644 (m-30) cc_final: 0.8345 (m-30) outliers start: 12 outliers final: 10 residues processed: 84 average time/residue: 0.1036 time to fit residues: 11.1992 Evaluate side-chains 84 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 131 SER Chi-restraints excluded: chain R residue 186 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 32 optimal weight: 0.1980 chunk 22 optimal weight: 9.9990 chunk 58 optimal weight: 0.0040 chunk 29 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 71 optimal weight: 0.0980 chunk 8 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.154820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.114959 restraints weight = 7764.256| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.31 r_work: 0.2947 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7159 Z= 0.090 Angle : 0.432 5.714 9709 Z= 0.234 Chirality : 0.039 0.140 1119 Planarity : 0.003 0.036 1208 Dihedral : 4.203 26.568 1057 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.21 % Allowed : 11.88 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.30), residues: 882 helix: 2.49 (0.28), residues: 384 sheet: 0.16 (0.38), residues: 184 loop : -0.59 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 219 TYR 0.006 0.001 TYR R 116 PHE 0.011 0.001 PHE A 189 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.000 HIS R 79 Details of bonding type rmsd covalent geometry : bond 0.00182 ( 7158) covalent geometry : angle 0.43206 ( 9707) SS BOND : bond 0.00050 ( 1) SS BOND : angle 0.58930 ( 2) hydrogen bonds : bond 0.03644 ( 365) hydrogen bonds : angle 4.13581 ( 1062) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.244 Fit side-chains REVERT: B 154 ASP cc_start: 0.8987 (OUTLIER) cc_final: 0.8757 (t0) REVERT: B 290 ASP cc_start: 0.8593 (m-30) cc_final: 0.8301 (m-30) outliers start: 9 outliers final: 7 residues processed: 84 average time/residue: 0.1188 time to fit residues: 12.6465 Evaluate side-chains 83 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 131 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 31 optimal weight: 0.0870 chunk 44 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 77 optimal weight: 0.1980 chunk 33 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.148503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.107347 restraints weight = 7835.744| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.25 r_work: 0.2959 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7159 Z= 0.095 Angle : 0.439 5.668 9709 Z= 0.238 Chirality : 0.040 0.134 1119 Planarity : 0.003 0.036 1208 Dihedral : 4.194 25.610 1057 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.35 % Allowed : 11.74 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.29), residues: 882 helix: 2.50 (0.28), residues: 384 sheet: 0.20 (0.38), residues: 184 loop : -0.60 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 219 TYR 0.006 0.001 TYR R 116 PHE 0.012 0.001 PHE A 189 TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS R 79 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 7158) covalent geometry : angle 0.43889 ( 9707) SS BOND : bond 0.00030 ( 1) SS BOND : angle 0.71094 ( 2) hydrogen bonds : bond 0.03735 ( 365) hydrogen bonds : angle 4.12929 ( 1062) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.213 Fit side-chains REVERT: B 154 ASP cc_start: 0.9009 (OUTLIER) cc_final: 0.8790 (t0) REVERT: B 290 ASP cc_start: 0.8602 (m-30) cc_final: 0.8295 (m-30) outliers start: 10 outliers final: 9 residues processed: 84 average time/residue: 0.0947 time to fit residues: 10.3303 Evaluate side-chains 82 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 131 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 50 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.146650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.106029 restraints weight = 7862.966| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.39 r_work: 0.2874 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7159 Z= 0.109 Angle : 0.457 5.739 9709 Z= 0.246 Chirality : 0.040 0.132 1119 Planarity : 0.003 0.036 1208 Dihedral : 4.305 25.471 1057 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.48 % Allowed : 12.01 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.29), residues: 882 helix: 2.46 (0.28), residues: 384 sheet: 0.14 (0.38), residues: 179 loop : -0.64 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.007 0.001 TYR B 59 PHE 0.013 0.001 PHE A 189 TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS R 79 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 7158) covalent geometry : angle 0.45645 ( 9707) SS BOND : bond 0.00030 ( 1) SS BOND : angle 0.90458 ( 2) hydrogen bonds : bond 0.04070 ( 365) hydrogen bonds : angle 4.18667 ( 1062) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.285 Fit side-chains REVERT: A 10 LYS cc_start: 0.7072 (tptt) cc_final: 0.6740 (tppt) REVERT: B 154 ASP cc_start: 0.8938 (OUTLIER) cc_final: 0.8712 (t0) REVERT: B 290 ASP cc_start: 0.8533 (m-30) cc_final: 0.8279 (m-30) outliers start: 11 outliers final: 10 residues processed: 82 average time/residue: 0.0999 time to fit residues: 10.6513 Evaluate side-chains 83 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 131 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 41 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 24 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.150596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.112194 restraints weight = 7773.622| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.21 r_work: 0.2863 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7159 Z= 0.107 Angle : 0.455 5.765 9709 Z= 0.245 Chirality : 0.040 0.145 1119 Planarity : 0.003 0.036 1208 Dihedral : 4.300 25.436 1057 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.62 % Allowed : 12.01 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.29), residues: 882 helix: 2.45 (0.28), residues: 384 sheet: 0.12 (0.38), residues: 179 loop : -0.63 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.007 0.001 TYR B 59 PHE 0.013 0.001 PHE A 189 TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS R 79 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 7158) covalent geometry : angle 0.45534 ( 9707) SS BOND : bond 0.00037 ( 1) SS BOND : angle 0.88600 ( 2) hydrogen bonds : bond 0.04055 ( 365) hydrogen bonds : angle 4.18575 ( 1062) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1987.46 seconds wall clock time: 34 minutes 37.58 seconds (2077.58 seconds total)