Starting phenix.real_space_refine on Wed Mar 4 00:16:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x5v_33016/03_2026/7x5v_33016_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x5v_33016/03_2026/7x5v_33016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x5v_33016/03_2026/7x5v_33016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x5v_33016/03_2026/7x5v_33016.map" model { file = "/net/cci-nas-00/data/ceres_data/7x5v_33016/03_2026/7x5v_33016_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x5v_33016/03_2026/7x5v_33016_neut.cif" } resolution = 2.83 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= 0.006 sd= 0.109 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 6263 2.51 5 N 1510 2.21 5 O 1675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 150 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9504 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2345 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 282} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2345 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 282} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2345 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 282} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2345 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 282} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 124 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Time building chain proxies: 2.16, per 1000 atoms: 0.23 Number of scatterers: 9504 At special positions: 0 Unit cell: (107.12, 108.16, 91.52, 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 56 16.00 O 1675 8.00 N 1510 7.00 C 6263 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: 0.67 Conformation dependent library (CDL) restraints added in 235.8 milliseconds 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2192 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 4 sheets defined 79.2% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.832A pdb=" N VAL A 76 " --> pdb=" O HIS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 107 Processing helix chain 'A' and resid 114 through 140 removed outlier: 3.937A pdb=" N TRP A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 172 removed outlier: 3.998A pdb=" N GLY A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 191 removed outlier: 3.583A pdb=" N MET A 179 " --> pdb=" O PRO A 176 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA A 180 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU A 181 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 184 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 186 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 187 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A 190 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 removed outlier: 4.129A pdb=" N ARG A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 237 Proline residue: A 212 - end of helix removed outlier: 4.378A pdb=" N ASN A 216 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALA A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 258 through 265 removed outlier: 3.754A pdb=" N VAL A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 290 through 303 Processing helix chain 'A' and resid 311 through 319 removed outlier: 4.068A pdb=" N ALA A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 337 Processing helix chain 'A' and resid 338 through 358 Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 82 through 107 Processing helix chain 'B' and resid 114 through 140 removed outlier: 3.937A pdb=" N TRP B 118 " --> pdb=" O TYR B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 172 removed outlier: 3.999A pdb=" N GLY B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 191 removed outlier: 3.584A pdb=" N MET B 179 " --> pdb=" O PRO B 176 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA B 180 " --> pdb=" O PRO B 177 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU B 181 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN B 184 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 186 " --> pdb=" O ARG B 183 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B 187 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 190 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 removed outlier: 4.128A pdb=" N ARG B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 237 Proline residue: B 212 - end of helix removed outlier: 4.378A pdb=" N ASN B 216 " --> pdb=" O PRO B 212 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS B 237 " --> pdb=" O VAL B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 265 removed outlier: 3.753A pdb=" N VAL B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 290 through 303 Processing helix chain 'B' and resid 311 through 319 removed outlier: 4.067A pdb=" N ALA B 315 " --> pdb=" O VAL B 311 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 319 " --> pdb=" O ALA B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 337 Processing helix chain 'B' and resid 338 through 358 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 82 through 107 Processing helix chain 'C' and resid 114 through 140 removed outlier: 3.938A pdb=" N TRP C 118 " --> pdb=" O TYR C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 172 removed outlier: 3.999A pdb=" N GLY C 172 " --> pdb=" O GLU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 191 removed outlier: 3.584A pdb=" N MET C 179 " --> pdb=" O PRO C 176 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA C 180 " --> pdb=" O PRO C 177 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU C 181 " --> pdb=" O SER C 178 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN C 184 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG C 186 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA C 187 " --> pdb=" O ASN C 184 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE C 190 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 removed outlier: 4.129A pdb=" N ARG C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 237 Proline residue: C 212 - end of helix removed outlier: 4.378A pdb=" N ASN C 216 " --> pdb=" O PRO C 212 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA C 217 " --> pdb=" O GLY C 213 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS C 237 " --> pdb=" O VAL C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 258 through 265 removed outlier: 3.753A pdb=" N VAL C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 289 Processing helix chain 'C' and resid 290 through 303 Processing helix chain 'C' and resid 311 through 319 removed outlier: 4.068A pdb=" N ALA C 315 " --> pdb=" O VAL C 311 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER C 319 " --> pdb=" O ALA C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 337 Processing helix chain 'C' and resid 338 through 358 Processing helix chain 'D' and resid 72 through 81 removed outlier: 3.832A pdb=" N VAL D 76 " --> pdb=" O HIS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 107 Processing helix chain 'D' and resid 114 through 140 removed outlier: 3.937A pdb=" N TRP D 118 " --> pdb=" O TYR D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 172 removed outlier: 3.998A pdb=" N GLY D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 191 removed outlier: 3.585A pdb=" N MET D 179 " --> pdb=" O PRO D 176 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA D 180 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU D 181 " --> pdb=" O SER D 178 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN D 184 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG D 186 " --> pdb=" O ARG D 183 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA D 187 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE D 190 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 removed outlier: 4.128A pdb=" N ARG D 196 " --> pdb=" O ARG D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 237 Proline residue: D 212 - end of helix removed outlier: 4.377A pdb=" N ASN D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ALA D 217 " --> pdb=" O GLY D 213 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 265 removed outlier: 3.752A pdb=" N VAL D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 289 Processing helix chain 'D' and resid 290 through 303 Processing helix chain 'D' and resid 311 through 319 removed outlier: 4.068A pdb=" N ALA D 315 " --> pdb=" O VAL D 311 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER D 319 " --> pdb=" O ALA D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 337 Processing helix chain 'D' and resid 338 through 358 Processing helix chain 'E' and resid 3 through 17 Processing sheet with id=AA1, first strand: chain 'A' and resid 244 through 248 Processing sheet with id=AA2, first strand: chain 'B' and resid 244 through 248 Processing sheet with id=AA3, first strand: chain 'C' and resid 244 through 248 Processing sheet with id=AA4, first strand: chain 'D' and resid 244 through 248 653 hydrogen bonds defined for protein. 1887 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: 1.38 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1489 1.31 - 1.44: 2983 1.44 - 1.56: 5208 1.56 - 1.68: 0 1.68 - 1.81: 88 Bond restraints: 9768 Sorted by residual: bond pdb=" CA THR D 244 " pdb=" C THR D 244 " ideal model delta sigma weight residual 1.520 1.474 0.047 1.22e-02 6.72e+03 1.48e+01 bond pdb=" N THR D 244 " pdb=" CA THR D 244 " ideal model delta sigma weight residual 1.455 1.416 0.039 1.25e-02 6.40e+03 9.80e+00 bond pdb=" C ASN D 251 " pdb=" O ASN D 251 " ideal model delta sigma weight residual 1.236 1.202 0.035 1.15e-02 7.56e+03 9.14e+00 bond pdb=" C ASP D 250 " pdb=" O ASP D 250 " ideal model delta sigma weight residual 1.230 1.187 0.044 1.56e-02 4.11e+03 7.84e+00 bond pdb=" CA ASN D 251 " pdb=" C ASN D 251 " ideal model delta sigma weight residual 1.524 1.493 0.031 1.27e-02 6.20e+03 6.00e+00 ... (remaining 9763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 12686 1.80 - 3.61: 465 3.61 - 5.41: 93 5.41 - 7.21: 17 7.21 - 9.02: 14 Bond angle restraints: 13275 Sorted by residual: angle pdb=" N HIS A 320 " pdb=" CA HIS A 320 " pdb=" C HIS A 320 " ideal model delta sigma weight residual 111.07 119.39 -8.32 1.07e+00 8.73e-01 6.05e+01 angle pdb=" N ASP C 250 " pdb=" CA ASP C 250 " pdb=" C ASP C 250 " ideal model delta sigma weight residual 111.71 102.69 9.02 1.34e+00 5.57e-01 4.53e+01 angle pdb=" N ASN C 251 " pdb=" CA ASN C 251 " pdb=" C ASN C 251 " ideal model delta sigma weight residual 111.07 117.57 -6.50 1.07e+00 8.73e-01 3.69e+01 angle pdb=" N ASN C 249 " pdb=" CA ASN C 249 " pdb=" C ASN C 249 " ideal model delta sigma weight residual 110.53 118.35 -7.82 1.29e+00 6.01e-01 3.68e+01 angle pdb=" N ARG B 146 " pdb=" CA ARG B 146 " pdb=" C ARG B 146 " ideal model delta sigma weight residual 112.23 119.74 -7.51 1.26e+00 6.30e-01 3.55e+01 ... (remaining 13270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 4957 17.13 - 34.26: 471 34.26 - 51.39: 104 51.39 - 68.53: 21 68.53 - 85.66: 8 Dihedral angle restraints: 5561 sinusoidal: 2130 harmonic: 3431 Sorted by residual: dihedral pdb=" C VAL D 252 " pdb=" N VAL D 252 " pdb=" CA VAL D 252 " pdb=" CB VAL D 252 " ideal model delta harmonic sigma weight residual -122.00 -133.38 11.38 0 2.50e+00 1.60e-01 2.07e+01 dihedral pdb=" CA TYR A 281 " pdb=" C TYR A 281 " pdb=" N THR A 282 " pdb=" CA THR A 282 " ideal model delta harmonic sigma weight residual 180.00 159.78 20.22 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA TYR B 281 " pdb=" C TYR B 281 " pdb=" N THR B 282 " pdb=" CA THR B 282 " ideal model delta harmonic sigma weight residual 180.00 159.79 20.21 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 5558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1254 0.071 - 0.142: 171 0.142 - 0.213: 19 0.213 - 0.284: 8 0.284 - 0.355: 2 Chirality restraints: 1454 Sorted by residual: chirality pdb=" CA VAL D 252 " pdb=" N VAL D 252 " pdb=" C VAL D 252 " pdb=" CB VAL D 252 " both_signs ideal model delta sigma weight residual False 2.44 2.09 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA TYR C 248 " pdb=" N TYR C 248 " pdb=" C TYR C 248 " pdb=" CB TYR C 248 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA LYS C 198 " pdb=" N LYS C 198 " pdb=" C LYS C 198 " pdb=" CB LYS C 198 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 1451 not shown) Planarity restraints: 1665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 338 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" C GLN A 338 " 0.053 2.00e-02 2.50e+03 pdb=" O GLN A 338 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE A 339 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 338 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" C GLN D 338 " -0.053 2.00e-02 2.50e+03 pdb=" O GLN D 338 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE D 339 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 338 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.36e+00 pdb=" C GLN B 338 " 0.053 2.00e-02 2.50e+03 pdb=" O GLN B 338 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE B 339 " -0.018 2.00e-02 2.50e+03 ... (remaining 1662 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 63 2.49 - 3.09: 7388 3.09 - 3.70: 14755 3.70 - 4.30: 21910 4.30 - 4.90: 35938 Nonbonded interactions: 80054 Sorted by model distance: nonbonded pdb=" OG1 THR A 247 " pdb=" OE1 GLN A 271 " model vdw 1.891 3.040 nonbonded pdb=" O HIS A 237 " pdb=" NH2 ARG C 254 " model vdw 1.930 3.120 nonbonded pdb=" OD1 ASN A 249 " pdb=" NE2 GLN A 271 " model vdw 1.981 3.120 nonbonded pdb=" O LEU B 328 " pdb=" OG SER B 332 " model vdw 2.155 3.040 nonbonded pdb=" O LEU D 328 " pdb=" OG SER D 332 " model vdw 2.156 3.040 ... (remaining 80049 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.430 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.500 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 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 0.072 9768 Z= 0.334 Angle : 0.867 9.017 13275 Z= 0.544 Chirality : 0.052 0.355 1454 Planarity : 0.005 0.043 1665 Dihedral : 14.746 85.658 3369 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.40 % Allowed : 15.43 % Favored : 83.17 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.21), residues: 1166 helix: -1.18 (0.15), residues: 786 sheet: -1.34 (0.59), residues: 48 loop : -2.03 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 254 TYR 0.014 0.002 TYR D 109 PHE 0.024 0.002 PHE D 144 TRP 0.012 0.002 TRP B 106 HIS 0.005 0.002 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00667 ( 9768) covalent geometry : angle 0.86698 (13275) hydrogen bonds : bond 0.13854 ( 653) hydrogen bonds : angle 6.87259 ( 1887) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 238 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 271 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7612 (pm20) REVERT: C 78 ASP cc_start: 0.7827 (m-30) cc_final: 0.7591 (m-30) REVERT: D 78 ASP cc_start: 0.7537 (m-30) cc_final: 0.7313 (m-30) REVERT: D 123 PHE cc_start: 0.6518 (t80) cc_final: 0.6185 (t80) REVERT: D 329 PHE cc_start: 0.7706 (t80) cc_final: 0.7498 (t80) outliers start: 14 outliers final: 11 residues processed: 251 average time/residue: 0.4901 time to fit residues: 131.9770 Evaluate side-chains 177 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 222 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 0.0370 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 266 GLN B 184 ASN B 201 ASN ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 320 HIS D 73 GLN D 136 ASN D 201 ASN D 266 GLN D 320 HIS E 7 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.189112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.141422 restraints weight = 9487.299| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.30 r_work: 0.3417 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9768 Z= 0.135 Angle : 0.562 5.954 13275 Z= 0.300 Chirality : 0.040 0.144 1454 Planarity : 0.004 0.026 1665 Dihedral : 5.698 59.551 1307 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.31 % Allowed : 18.64 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.25), residues: 1166 helix: 0.64 (0.18), residues: 782 sheet: -0.54 (0.64), residues: 48 loop : -0.84 (0.39), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 196 TYR 0.014 0.001 TYR D 245 PHE 0.026 0.001 PHE A 144 TRP 0.020 0.001 TRP B 145 HIS 0.003 0.001 HIS D 237 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9768) covalent geometry : angle 0.56188 (13275) hydrogen bonds : bond 0.04243 ( 653) hydrogen bonds : angle 5.32456 ( 1887) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 SER cc_start: 0.8500 (m) cc_final: 0.8221 (p) REVERT: B 133 LEU cc_start: 0.7864 (tp) cc_final: 0.7624 (tp) REVERT: B 143 CYS cc_start: 0.6202 (OUTLIER) cc_final: 0.5654 (t) REVERT: B 186 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.6944 (ptm160) REVERT: B 253 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7805 (tppt) REVERT: B 269 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7667 (mt) REVERT: C 271 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7759 (pm20) REVERT: D 123 PHE cc_start: 0.6694 (t80) cc_final: 0.6248 (t80) REVERT: D 143 CYS cc_start: 0.5144 (OUTLIER) cc_final: 0.4088 (t) REVERT: D 148 ASN cc_start: 0.8479 (t0) cc_final: 0.8030 (t0) REVERT: D 329 PHE cc_start: 0.7896 (t80) cc_final: 0.7686 (t80) REVERT: D 348 VAL cc_start: 0.8608 (p) cc_final: 0.8341 (m) REVERT: D 352 LYS cc_start: 0.8046 (tppt) cc_final: 0.7781 (mptt) outliers start: 43 outliers final: 15 residues processed: 219 average time/residue: 0.3944 time to fit residues: 93.9651 Evaluate side-chains 184 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 222 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 7 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 115 GLN A 136 ASN A 184 ASN A 249 ASN A 266 GLN B 115 GLN B 266 GLN C 115 GLN D 266 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.184471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.127028 restraints weight = 9466.651| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.82 r_work: 0.3358 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9768 Z= 0.154 Angle : 0.555 6.256 13275 Z= 0.296 Chirality : 0.040 0.154 1454 Planarity : 0.004 0.041 1665 Dihedral : 4.614 41.294 1294 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.61 % Allowed : 20.34 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.25), residues: 1166 helix: 1.02 (0.18), residues: 782 sheet: -0.40 (0.68), residues: 48 loop : -0.54 (0.40), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 196 TYR 0.013 0.001 TYR D 109 PHE 0.024 0.002 PHE A 144 TRP 0.010 0.001 TRP C 106 HIS 0.005 0.001 HIS D 320 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9768) covalent geometry : angle 0.55510 (13275) hydrogen bonds : bond 0.04359 ( 653) hydrogen bonds : angle 5.16386 ( 1887) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 SER cc_start: 0.8587 (m) cc_final: 0.8246 (p) REVERT: B 133 LEU cc_start: 0.7704 (tp) cc_final: 0.7270 (tp) REVERT: B 137 PHE cc_start: 0.8203 (m-10) cc_final: 0.7727 (m-80) REVERT: B 143 CYS cc_start: 0.5711 (OUTLIER) cc_final: 0.5210 (t) REVERT: B 175 MET cc_start: 0.6595 (mmt) cc_final: 0.6350 (mtt) REVERT: B 186 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6862 (ptm160) REVERT: B 253 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7990 (tppt) REVERT: C 143 CYS cc_start: 0.5537 (OUTLIER) cc_final: 0.4546 (t) REVERT: D 143 CYS cc_start: 0.5299 (OUTLIER) cc_final: 0.4337 (t) REVERT: D 148 ASN cc_start: 0.8559 (t0) cc_final: 0.8349 (m-40) REVERT: D 271 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7982 (pm20) REVERT: D 329 PHE cc_start: 0.7965 (t80) cc_final: 0.7761 (t80) REVERT: D 352 LYS cc_start: 0.7985 (tppt) cc_final: 0.7710 (mptt) outliers start: 36 outliers final: 12 residues processed: 187 average time/residue: 0.4075 time to fit residues: 82.7464 Evaluate side-chains 174 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 271 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 77 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 115 GLN A 266 GLN B 96 ASN B 115 GLN B 266 GLN C 96 ASN C 115 GLN D 266 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.177493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.120349 restraints weight = 9716.478| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.81 r_work: 0.3339 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9768 Z= 0.134 Angle : 0.529 6.775 13275 Z= 0.281 Chirality : 0.039 0.148 1454 Planarity : 0.004 0.037 1665 Dihedral : 4.451 37.651 1292 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.61 % Allowed : 21.14 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.25), residues: 1166 helix: 1.00 (0.18), residues: 826 sheet: -0.41 (0.65), residues: 48 loop : -1.01 (0.40), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 196 TYR 0.011 0.001 TYR D 109 PHE 0.023 0.001 PHE A 144 TRP 0.009 0.001 TRP C 145 HIS 0.004 0.001 HIS D 320 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9768) covalent geometry : angle 0.52891 (13275) hydrogen bonds : bond 0.04056 ( 653) hydrogen bonds : angle 5.01794 ( 1887) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 SER cc_start: 0.8593 (m) cc_final: 0.8304 (p) REVERT: A 342 ILE cc_start: 0.8255 (mm) cc_final: 0.8010 (mt) REVERT: B 132 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7948 (tp30) REVERT: B 133 LEU cc_start: 0.7659 (tp) cc_final: 0.7301 (tp) REVERT: B 137 PHE cc_start: 0.8202 (m-10) cc_final: 0.7708 (m-80) REVERT: B 253 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8057 (tppt) REVERT: B 342 ILE cc_start: 0.8367 (mm) cc_final: 0.8151 (mt) REVERT: C 96 ASN cc_start: 0.8206 (t0) cc_final: 0.7900 (t0) REVERT: C 133 LEU cc_start: 0.7722 (tp) cc_final: 0.7388 (tp) REVERT: C 143 CYS cc_start: 0.5575 (OUTLIER) cc_final: 0.4608 (t) REVERT: C 266 GLN cc_start: 0.7744 (mt0) cc_final: 0.7470 (mm-40) REVERT: C 342 ILE cc_start: 0.8173 (mm) cc_final: 0.7895 (mt) REVERT: D 128 MET cc_start: 0.8317 (mtt) cc_final: 0.8028 (mtm) REVERT: D 143 CYS cc_start: 0.5304 (OUTLIER) cc_final: 0.4390 (t) REVERT: D 352 LYS cc_start: 0.7957 (tppt) cc_final: 0.7691 (mptt) outliers start: 36 outliers final: 16 residues processed: 192 average time/residue: 0.3821 time to fit residues: 80.2193 Evaluate side-chains 178 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 143 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 35 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 69 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 115 GLN A 266 GLN B 115 GLN B 266 GLN C 115 GLN C 249 ASN D 266 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.174836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.117125 restraints weight = 9764.170| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.81 r_work: 0.3321 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9768 Z= 0.184 Angle : 0.567 7.271 13275 Z= 0.302 Chirality : 0.041 0.151 1454 Planarity : 0.004 0.044 1665 Dihedral : 4.462 35.854 1292 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.91 % Allowed : 21.14 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.25), residues: 1166 helix: 1.23 (0.18), residues: 794 sheet: -0.35 (0.63), residues: 48 loop : -0.38 (0.41), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 196 TYR 0.014 0.002 TYR D 109 PHE 0.024 0.002 PHE A 144 TRP 0.011 0.002 TRP C 106 HIS 0.004 0.001 HIS D 320 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 9768) covalent geometry : angle 0.56680 (13275) hydrogen bonds : bond 0.04481 ( 653) hydrogen bonds : angle 5.16645 ( 1887) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.7544 (tp) cc_final: 0.7320 (tp) REVERT: A 268 SER cc_start: 0.8635 (m) cc_final: 0.8316 (p) REVERT: A 342 ILE cc_start: 0.8316 (mm) cc_final: 0.8064 (mt) REVERT: B 132 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7895 (tp30) REVERT: B 133 LEU cc_start: 0.7636 (tp) cc_final: 0.7191 (tp) REVERT: B 137 PHE cc_start: 0.8246 (m-10) cc_final: 0.7746 (m-80) REVERT: B 253 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8121 (tttt) REVERT: B 342 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8118 (mt) REVERT: C 132 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8163 (tp30) REVERT: C 137 PHE cc_start: 0.8446 (m-10) cc_final: 0.8241 (m-10) REVERT: C 143 CYS cc_start: 0.5579 (OUTLIER) cc_final: 0.4722 (t) REVERT: C 342 ILE cc_start: 0.8229 (mm) cc_final: 0.7956 (mt) REVERT: D 133 LEU cc_start: 0.7654 (tp) cc_final: 0.7443 (OUTLIER) REVERT: D 137 PHE cc_start: 0.8469 (m-10) cc_final: 0.8257 (m-10) REVERT: D 352 LYS cc_start: 0.7943 (mppt) cc_final: 0.7673 (mptt) outliers start: 39 outliers final: 17 residues processed: 192 average time/residue: 0.3925 time to fit residues: 82.2032 Evaluate side-chains 187 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 250 ASP Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 43 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 115 GLN A 266 GLN B 115 GLN B 266 GLN C 115 GLN C 249 ASN D 266 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.177399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.120158 restraints weight = 9690.861| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.83 r_work: 0.3201 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9768 Z= 0.148 Angle : 0.538 6.729 13275 Z= 0.285 Chirality : 0.039 0.148 1454 Planarity : 0.004 0.038 1665 Dihedral : 4.345 34.814 1292 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.21 % Allowed : 21.54 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.25), residues: 1166 helix: 1.09 (0.18), residues: 826 sheet: -0.16 (0.61), residues: 48 loop : -1.06 (0.40), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 196 TYR 0.012 0.001 TYR B 109 PHE 0.024 0.001 PHE D 144 TRP 0.007 0.001 TRP C 106 HIS 0.003 0.001 HIS C 237 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9768) covalent geometry : angle 0.53819 (13275) hydrogen bonds : bond 0.04153 ( 653) hydrogen bonds : angle 5.06638 ( 1887) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 164 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8355 (mtm) cc_final: 0.8092 (mtt) REVERT: A 268 SER cc_start: 0.8666 (m) cc_final: 0.8344 (p) REVERT: A 342 ILE cc_start: 0.8340 (mm) cc_final: 0.8079 (mt) REVERT: B 179 MET cc_start: 0.5867 (pmm) cc_final: 0.5162 (tpp) REVERT: B 209 LYS cc_start: 0.7826 (mtpp) cc_final: 0.7228 (mtpm) REVERT: B 253 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8129 (tttt) REVERT: B 342 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8087 (mt) REVERT: C 133 LEU cc_start: 0.7621 (tp) cc_final: 0.7313 (tp) REVERT: C 137 PHE cc_start: 0.8352 (m-10) cc_final: 0.8110 (m-10) REVERT: C 143 CYS cc_start: 0.5543 (OUTLIER) cc_final: 0.4687 (t) REVERT: C 266 GLN cc_start: 0.7768 (mt0) cc_final: 0.7410 (mm-40) REVERT: D 137 PHE cc_start: 0.8445 (m-10) cc_final: 0.8197 (m-10) REVERT: D 352 LYS cc_start: 0.7890 (mppt) cc_final: 0.7605 (mptt) outliers start: 42 outliers final: 19 residues processed: 186 average time/residue: 0.3992 time to fit residues: 80.8936 Evaluate side-chains 182 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 258 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 112 optimal weight: 0.0980 chunk 45 optimal weight: 0.2980 chunk 100 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 115 GLN A 266 GLN B 115 GLN B 266 GLN C 115 GLN C 249 ASN D 266 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.177820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.121358 restraints weight = 9763.549| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.83 r_work: 0.3239 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9768 Z= 0.123 Angle : 0.523 6.245 13275 Z= 0.276 Chirality : 0.038 0.149 1454 Planarity : 0.004 0.031 1665 Dihedral : 4.214 29.820 1291 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.61 % Allowed : 23.15 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.25), residues: 1166 helix: 1.24 (0.18), residues: 826 sheet: -0.04 (0.63), residues: 48 loop : -0.98 (0.41), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 196 TYR 0.009 0.001 TYR D 109 PHE 0.025 0.001 PHE A 137 TRP 0.007 0.001 TRP D 145 HIS 0.003 0.001 HIS D 320 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9768) covalent geometry : angle 0.52270 (13275) hydrogen bonds : bond 0.03857 ( 653) hydrogen bonds : angle 4.93926 ( 1887) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8330 (mtm) cc_final: 0.8075 (mtt) REVERT: A 268 SER cc_start: 0.8602 (m) cc_final: 0.8332 (p) REVERT: A 342 ILE cc_start: 0.8322 (mm) cc_final: 0.8060 (mt) REVERT: B 132 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8062 (tp30) REVERT: B 179 MET cc_start: 0.5753 (pmm) cc_final: 0.5171 (tpp) REVERT: B 209 LYS cc_start: 0.7853 (mtpp) cc_final: 0.7296 (mtpm) REVERT: B 286 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: B 342 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8129 (mt) REVERT: C 132 GLU cc_start: 0.8342 (tp30) cc_final: 0.8106 (tp30) REVERT: C 137 PHE cc_start: 0.8301 (m-10) cc_final: 0.8048 (m-10) REVERT: C 261 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7796 (mt-10) REVERT: C 266 GLN cc_start: 0.7806 (mt0) cc_final: 0.7397 (mm-40) REVERT: D 342 ILE cc_start: 0.8223 (mm) cc_final: 0.7949 (mt) REVERT: D 352 LYS cc_start: 0.7944 (mppt) cc_final: 0.7656 (mptt) outliers start: 26 outliers final: 10 residues processed: 176 average time/residue: 0.4001 time to fit residues: 76.5915 Evaluate side-chains 168 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain D residue 114 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 103 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 115 GLN A 266 GLN B 115 GLN B 266 GLN C 115 GLN C 249 ASN D 266 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.176221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119488 restraints weight = 9750.707| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.82 r_work: 0.3324 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9768 Z= 0.145 Angle : 0.554 7.815 13275 Z= 0.291 Chirality : 0.039 0.146 1454 Planarity : 0.004 0.036 1665 Dihedral : 4.216 26.331 1291 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.71 % Allowed : 23.35 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.25), residues: 1166 helix: 1.17 (0.18), residues: 826 sheet: -0.13 (0.65), residues: 48 loop : -1.00 (0.41), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 196 TYR 0.011 0.001 TYR D 109 PHE 0.028 0.002 PHE D 137 TRP 0.007 0.001 TRP C 106 HIS 0.003 0.001 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9768) covalent geometry : angle 0.55433 (13275) hydrogen bonds : bond 0.04041 ( 653) hydrogen bonds : angle 5.01024 ( 1887) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8369 (mtm) cc_final: 0.8112 (mtt) REVERT: A 268 SER cc_start: 0.8536 (m) cc_final: 0.8268 (p) REVERT: A 342 ILE cc_start: 0.8357 (mm) cc_final: 0.8104 (mt) REVERT: B 179 MET cc_start: 0.5599 (pmm) cc_final: 0.5089 (tpp) REVERT: B 209 LYS cc_start: 0.7823 (mtpp) cc_final: 0.7255 (mtpm) REVERT: B 286 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8236 (tt0) REVERT: B 342 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8164 (mt) REVERT: C 261 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7848 (mt-10) REVERT: C 266 GLN cc_start: 0.7718 (mt0) cc_final: 0.7420 (mm-40) REVERT: D 209 LYS cc_start: 0.7882 (mttp) cc_final: 0.7275 (mtpm) REVERT: D 342 ILE cc_start: 0.8280 (mm) cc_final: 0.8032 (mt) REVERT: D 352 LYS cc_start: 0.7998 (mppt) cc_final: 0.7753 (mptt) outliers start: 27 outliers final: 15 residues processed: 171 average time/residue: 0.4314 time to fit residues: 80.1259 Evaluate side-chains 164 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 250 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 68 optimal weight: 0.0870 chunk 13 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 115 GLN A 266 GLN B 115 GLN B 266 GLN C 115 GLN C 249 ASN D 266 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.176856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.120569 restraints weight = 9731.062| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.80 r_work: 0.3242 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9768 Z= 0.134 Angle : 0.549 7.282 13275 Z= 0.287 Chirality : 0.038 0.143 1454 Planarity : 0.004 0.033 1665 Dihedral : 4.194 24.076 1291 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.80 % Allowed : 24.35 % Favored : 73.85 % 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 are not related in a simple way. whole: 0.87 (0.25), residues: 1166 helix: 1.20 (0.18), residues: 826 sheet: -0.10 (0.66), residues: 48 loop : -0.99 (0.41), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 196 TYR 0.010 0.001 TYR D 109 PHE 0.033 0.002 PHE C 137 TRP 0.008 0.001 TRP B 145 HIS 0.003 0.001 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9768) covalent geometry : angle 0.54894 (13275) hydrogen bonds : bond 0.03919 ( 653) hydrogen bonds : angle 4.98308 ( 1887) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.6779 (ttp-110) cc_final: 0.6555 (ttp80) REVERT: A 128 MET cc_start: 0.8303 (mtm) cc_final: 0.8040 (mtt) REVERT: A 268 SER cc_start: 0.8479 (m) cc_final: 0.8201 (p) REVERT: A 342 ILE cc_start: 0.8299 (mm) cc_final: 0.8040 (mt) REVERT: B 179 MET cc_start: 0.5849 (pmm) cc_final: 0.5189 (tpp) REVERT: B 209 LYS cc_start: 0.7742 (mtpp) cc_final: 0.7349 (mtpm) REVERT: B 286 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8214 (tt0) REVERT: B 342 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8132 (mt) REVERT: C 209 LYS cc_start: 0.7692 (mttm) cc_final: 0.7234 (mtmm) REVERT: C 261 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7720 (mt-10) REVERT: C 266 GLN cc_start: 0.7694 (mt0) cc_final: 0.7362 (mm-40) REVERT: C 342 ILE cc_start: 0.8252 (mm) cc_final: 0.8014 (mt) REVERT: D 209 LYS cc_start: 0.7759 (mttp) cc_final: 0.7208 (mtpm) REVERT: D 342 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8048 (mt) REVERT: D 352 LYS cc_start: 0.7860 (mppt) cc_final: 0.7620 (mptt) outliers start: 18 outliers final: 10 residues processed: 167 average time/residue: 0.4330 time to fit residues: 78.3165 Evaluate side-chains 164 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 342 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 1 optimal weight: 0.0980 chunk 86 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 107 optimal weight: 0.0270 chunk 111 optimal weight: 0.0980 chunk 77 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 115 GLN A 266 GLN B 115 GLN B 266 GLN C 115 GLN C 249 ASN D 184 ASN D 266 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.178675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.122707 restraints weight = 9719.965| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.82 r_work: 0.3261 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9768 Z= 0.121 Angle : 0.547 7.216 13275 Z= 0.284 Chirality : 0.037 0.141 1454 Planarity : 0.004 0.029 1665 Dihedral : 4.109 18.840 1290 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.80 % Allowed : 24.45 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.25), residues: 1166 helix: 1.25 (0.18), residues: 826 sheet: -0.05 (0.68), residues: 48 loop : -0.99 (0.41), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 196 TYR 0.008 0.001 TYR D 245 PHE 0.023 0.001 PHE D 137 TRP 0.009 0.001 TRP D 145 HIS 0.003 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9768) covalent geometry : angle 0.54694 (13275) hydrogen bonds : bond 0.03733 ( 653) hydrogen bonds : angle 4.91418 ( 1887) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8381 (mtm) cc_final: 0.8090 (mtt) REVERT: A 268 SER cc_start: 0.8413 (m) cc_final: 0.8181 (p) REVERT: A 342 ILE cc_start: 0.8299 (mm) cc_final: 0.8043 (mt) REVERT: B 179 MET cc_start: 0.5818 (pmm) cc_final: 0.5219 (tpp) REVERT: B 209 LYS cc_start: 0.7765 (mtpp) cc_final: 0.7391 (mtpm) REVERT: B 286 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8208 (tt0) REVERT: B 342 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8130 (mt) REVERT: C 209 LYS cc_start: 0.7770 (mttm) cc_final: 0.7328 (mtmm) REVERT: C 261 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7759 (mt-10) REVERT: C 266 GLN cc_start: 0.7765 (mt0) cc_final: 0.7418 (mm-40) REVERT: C 342 ILE cc_start: 0.8260 (mm) cc_final: 0.8032 (mt) REVERT: D 209 LYS cc_start: 0.7875 (mttp) cc_final: 0.7311 (mtpm) REVERT: D 342 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8070 (mt) REVERT: D 352 LYS cc_start: 0.7912 (mppt) cc_final: 0.7670 (mptt) outliers start: 18 outliers final: 9 residues processed: 171 average time/residue: 0.4235 time to fit residues: 78.7801 Evaluate side-chains 165 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 342 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 0.0770 chunk 50 optimal weight: 0.5980 chunk 105 optimal weight: 0.2980 chunk 3 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 97 optimal weight: 10.0000 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 115 GLN A 266 GLN B 115 GLN B 266 GLN C 115 GLN C 249 ASN D 266 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.178635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.122650 restraints weight = 9732.111| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.83 r_work: 0.3373 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9768 Z= 0.124 Angle : 0.541 7.233 13275 Z= 0.282 Chirality : 0.038 0.141 1454 Planarity : 0.004 0.026 1665 Dihedral : 4.078 18.536 1290 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.50 % Allowed : 25.25 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.25), residues: 1166 helix: 1.26 (0.18), residues: 826 sheet: -0.13 (0.69), residues: 48 loop : -1.01 (0.40), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 196 TYR 0.011 0.001 TYR C 248 PHE 0.024 0.001 PHE C 137 TRP 0.009 0.001 TRP B 145 HIS 0.003 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9768) covalent geometry : angle 0.54122 (13275) hydrogen bonds : bond 0.03733 ( 653) hydrogen bonds : angle 4.90756 ( 1887) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3620.92 seconds wall clock time: 62 minutes 18.59 seconds (3738.59 seconds total)