Starting phenix.real_space_refine on Fri Mar 14 02:26:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x5v_33016/03_2025/7x5v_33016_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x5v_33016/03_2025/7x5v_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_2025/7x5v_33016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x5v_33016/03_2025/7x5v_33016.map" model { file = "/net/cci-nas-00/data/ceres_data/7x5v_33016/03_2025/7x5v_33016_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x5v_33016/03_2025/7x5v_33016_neut.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.75, per 1000 atoms: 0.61 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: 2.27 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.85 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: 2.63 Time building geometry restraints manager: 2.68 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: 1.130 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: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.630 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.860 ------------------------------------------------------------------------------- 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= 0.425 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (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 TRP 0.012 0.002 TRP B 106 HIS 0.005 0.002 HIS A 320 PHE 0.024 0.002 PHE D 144 TYR 0.014 0.002 TYR D 109 ARG 0.005 0.001 ARG C 254 *********************** 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 : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 271 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7614 (pm20) REVERT: C 78 ASP cc_start: 0.7827 (m-30) cc_final: 0.7590 (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: 0.6189 (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: 1.3154 time to fit residues: 355.5332 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 : 1.172 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 68 optimal weight: 0.0980 chunk 106 optimal weight: 3.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 115 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.189644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.141486 restraints weight = 9356.381| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.13 r_work: 0.3432 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2241 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= 0.176 Angle : 0.561 6.272 13275 Z= 0.299 Chirality : 0.039 0.145 1454 Planarity : 0.004 0.024 1665 Dihedral : 5.723 59.596 1307 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.31 % Allowed : 19.14 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1166 helix: 0.67 (0.18), residues: 782 sheet: -0.52 (0.65), residues: 48 loop : -0.87 (0.39), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 145 HIS 0.003 0.001 HIS A 237 PHE 0.025 0.001 PHE A 144 TYR 0.014 0.001 TYR D 245 ARG 0.004 0.001 ARG B 196 *********************** 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 231 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8331 (mtm) cc_final: 0.8067 (mtm) REVERT: A 268 SER cc_start: 0.8500 (m) cc_final: 0.8225 (p) REVERT: B 133 LEU cc_start: 0.7805 (tp) cc_final: 0.7561 (tp) REVERT: B 143 CYS cc_start: 0.6171 (OUTLIER) cc_final: 0.5620 (t) REVERT: B 186 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6903 (ptm160) REVERT: B 269 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7582 (mt) REVERT: D 123 PHE cc_start: 0.6631 (t80) cc_final: 0.6141 (t80) REVERT: D 148 ASN cc_start: 0.8494 (t0) cc_final: 0.8033 (t0) REVERT: D 348 VAL cc_start: 0.8563 (p) cc_final: 0.8278 (m) REVERT: D 352 LYS cc_start: 0.7985 (tppt) cc_final: 0.7693 (mptt) outliers start: 43 outliers final: 15 residues processed: 218 average time/residue: 1.0882 time to fit residues: 259.6127 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 : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 258 THR 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 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 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 43 optimal weight: 0.1980 chunk 14 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 29 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 266 GLN B 266 GLN C 115 GLN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.187405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.130313 restraints weight = 9508.419| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.81 r_work: 0.3392 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9768 Z= 0.181 Angle : 0.531 6.624 13275 Z= 0.280 Chirality : 0.039 0.171 1454 Planarity : 0.004 0.037 1665 Dihedral : 4.616 45.084 1294 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.81 % Allowed : 20.04 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1166 helix: 1.16 (0.18), residues: 778 sheet: -0.26 (0.67), residues: 48 loop : -0.53 (0.40), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 145 HIS 0.004 0.001 HIS D 320 PHE 0.023 0.001 PHE A 144 TYR 0.010 0.001 TYR D 245 ARG 0.006 0.001 ARG A 196 *********************** 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 211 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 ASP cc_start: 0.8322 (t0) cc_final: 0.8100 (t0) REVERT: A 268 SER cc_start: 0.8515 (m) cc_final: 0.8227 (p) REVERT: A 342 ILE cc_start: 0.8218 (mm) cc_final: 0.7960 (mt) REVERT: B 133 LEU cc_start: 0.7690 (tp) cc_final: 0.7344 (tp) REVERT: B 137 PHE cc_start: 0.8146 (m-10) cc_final: 0.7671 (m-80) REVERT: B 143 CYS cc_start: 0.5610 (OUTLIER) cc_final: 0.5202 (t) REVERT: B 175 MET cc_start: 0.6654 (OUTLIER) cc_final: 0.6357 (mtt) REVERT: B 186 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6891 (ptm160) REVERT: B 253 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7900 (tttt) REVERT: C 105 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7372 (tp30) REVERT: C 143 CYS cc_start: 0.5472 (OUTLIER) cc_final: 0.4458 (t) REVERT: C 266 GLN cc_start: 0.7552 (mt0) cc_final: 0.7297 (mm-40) REVERT: C 342 ILE cc_start: 0.8207 (mm) cc_final: 0.7878 (mt) REVERT: D 123 PHE cc_start: 0.6580 (t80) cc_final: 0.6150 (t80) REVERT: D 132 GLU cc_start: 0.8087 (tt0) cc_final: 0.7877 (tp30) REVERT: D 143 CYS cc_start: 0.5289 (OUTLIER) cc_final: 0.4263 (t) REVERT: D 148 ASN cc_start: 0.8605 (t0) cc_final: 0.8398 (m-40) REVERT: D 271 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7874 (pm20) REVERT: D 352 LYS cc_start: 0.7974 (tppt) cc_final: 0.7716 (mptt) outliers start: 38 outliers final: 12 residues processed: 198 average time/residue: 0.9298 time to fit residues: 201.0924 Evaluate side-chains 179 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 250 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 175 MET 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 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 100 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 97 optimal weight: 30.0000 chunk 69 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 D 266 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.177372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.119409 restraints weight = 9518.028| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.80 r_work: 0.3304 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9768 Z= 0.251 Angle : 0.556 6.569 13275 Z= 0.296 Chirality : 0.040 0.148 1454 Planarity : 0.004 0.044 1665 Dihedral : 4.503 42.285 1292 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.71 % Allowed : 21.44 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.25), residues: 1166 helix: 1.21 (0.18), residues: 794 sheet: -0.48 (0.65), residues: 48 loop : -0.40 (0.41), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 106 HIS 0.004 0.001 HIS D 320 PHE 0.024 0.002 PHE A 144 TYR 0.014 0.002 TYR D 109 ARG 0.004 0.001 ARG D 196 *********************** 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 205 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 168 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.5430 (pmm) cc_final: 0.4998 (tpp) REVERT: A 268 SER cc_start: 0.8594 (m) cc_final: 0.8302 (p) REVERT: A 342 ILE cc_start: 0.8266 (mm) cc_final: 0.8023 (mt) REVERT: B 122 GLU cc_start: 0.6296 (OUTLIER) cc_final: 0.6032 (tp30) REVERT: B 133 LEU cc_start: 0.7683 (tp) cc_final: 0.7295 (tp) REVERT: B 137 PHE cc_start: 0.8241 (m-10) cc_final: 0.7807 (m-80) REVERT: B 186 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.7068 (ptm160) REVERT: B 253 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8098 (tttt) REVERT: C 143 CYS cc_start: 0.5711 (OUTLIER) cc_final: 0.4757 (t) REVERT: C 342 ILE cc_start: 0.8275 (mm) cc_final: 0.7976 (mt) REVERT: D 352 LYS cc_start: 0.7986 (mppt) cc_final: 0.7719 (mptt) outliers start: 37 outliers final: 14 residues processed: 191 average time/residue: 0.9007 time to fit residues: 187.9231 Evaluate side-chains 177 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 114 TYR Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 143 CYS 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 1 optimal weight: 0.9990 chunk 40 optimal weight: 0.0970 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 96 ASN C 115 GLN C 249 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 = 0.4017 r_free = 0.4017 target = 0.178093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.120969 restraints weight = 9573.255| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.80 r_work: 0.3240 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3337 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= 0.179 Angle : 0.524 7.079 13275 Z= 0.274 Chirality : 0.038 0.151 1454 Planarity : 0.004 0.031 1665 Dihedral : 4.328 37.544 1292 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.31 % Allowed : 22.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.25), residues: 1166 helix: 1.15 (0.18), residues: 826 sheet: -0.16 (0.64), residues: 48 loop : -1.01 (0.40), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 145 HIS 0.003 0.001 HIS D 320 PHE 0.023 0.001 PHE D 144 TYR 0.010 0.001 TYR D 109 ARG 0.004 0.000 ARG D 196 *********************** 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 201 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8307 (mtm) cc_final: 0.8058 (mtt) REVERT: A 133 LEU cc_start: 0.7590 (tp) cc_final: 0.7382 (tp) REVERT: A 179 MET cc_start: 0.5360 (pmm) cc_final: 0.4967 (tpp) REVERT: A 209 LYS cc_start: 0.7871 (mttm) cc_final: 0.7285 (mtpm) REVERT: A 268 SER cc_start: 0.8618 (m) cc_final: 0.8324 (p) REVERT: A 342 ILE cc_start: 0.8328 (mm) cc_final: 0.8076 (mt) REVERT: B 133 LEU cc_start: 0.7583 (tp) cc_final: 0.7197 (tp) REVERT: B 137 PHE cc_start: 0.8155 (m-10) cc_final: 0.7738 (m-80) REVERT: B 155 ASP cc_start: 0.7279 (t0) cc_final: 0.7034 (t0) REVERT: B 186 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6970 (ptm-80) REVERT: B 234 GLU cc_start: 0.7723 (tp30) cc_final: 0.7435 (mt-10) REVERT: B 253 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8086 (tttt) REVERT: B 342 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8114 (mt) REVERT: C 128 MET cc_start: 0.8348 (mtm) cc_final: 0.8122 (mtt) REVERT: C 143 CYS cc_start: 0.5488 (OUTLIER) cc_final: 0.4581 (t) REVERT: C 266 GLN cc_start: 0.7735 (mt0) cc_final: 0.7411 (mm-40) REVERT: D 342 ILE cc_start: 0.8219 (mm) cc_final: 0.7925 (mt) REVERT: D 352 LYS cc_start: 0.7919 (mppt) cc_final: 0.7648 (mptt) outliers start: 33 outliers final: 14 residues processed: 187 average time/residue: 0.9249 time to fit residues: 189.3437 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 : 1.055 ------------------------------------------------------------------------------- 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 306 SER Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 143 CYS 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 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 247 THR Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 143 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 17 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 105 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 47 optimal weight: 0.0870 chunk 54 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 D 266 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.177814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.120989 restraints weight = 9664.827| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.81 r_work: 0.3368 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3470 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= 0.183 Angle : 0.525 7.686 13275 Z= 0.276 Chirality : 0.038 0.147 1454 Planarity : 0.004 0.032 1665 Dihedral : 4.272 31.201 1292 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.01 % Allowed : 22.85 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.25), residues: 1166 helix: 1.23 (0.18), residues: 826 sheet: -0.07 (0.63), residues: 48 loop : -0.97 (0.40), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 145 HIS 0.003 0.001 HIS D 320 PHE 0.025 0.001 PHE D 329 TYR 0.010 0.001 TYR B 109 ARG 0.004 0.000 ARG D 196 *********************** 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 197 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8315 (mtm) cc_final: 0.8059 (mtt) REVERT: A 179 MET cc_start: 0.5376 (pmm) cc_final: 0.5076 (tpp) REVERT: A 209 LYS cc_start: 0.7687 (mttm) cc_final: 0.7206 (mtmm) REVERT: A 268 SER cc_start: 0.8597 (m) cc_final: 0.8303 (p) REVERT: A 342 ILE cc_start: 0.8332 (mm) cc_final: 0.8080 (mt) REVERT: B 132 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7994 (tp30) REVERT: B 133 LEU cc_start: 0.7520 (tp) cc_final: 0.7210 (tp) REVERT: B 137 PHE cc_start: 0.8173 (m-10) cc_final: 0.7762 (m-80) REVERT: B 186 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.7026 (ptm160) REVERT: B 209 LYS cc_start: 0.7767 (mtpp) cc_final: 0.7188 (mtpm) REVERT: B 234 GLU cc_start: 0.7646 (tp30) cc_final: 0.7365 (mt-10) REVERT: B 342 ILE cc_start: 0.8361 (mm) cc_final: 0.8141 (mt) REVERT: C 105 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7330 (tp30) REVERT: C 132 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7923 (tp30) REVERT: C 261 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7804 (mt-10) REVERT: C 266 GLN cc_start: 0.7746 (mt0) cc_final: 0.7408 (mm-40) REVERT: D 342 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.8040 (mt) REVERT: D 352 LYS cc_start: 0.7943 (mppt) cc_final: 0.7662 (mptt) outliers start: 30 outliers final: 16 residues processed: 184 average time/residue: 0.9216 time to fit residues: 185.5391 Evaluate side-chains 179 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 306 SER Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain C residue 105 GLU 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 250 ASP Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 342 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 8 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.180159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.132532 restraints weight = 9618.095| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.38 r_work: 0.3355 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3572 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= 0.202 Angle : 0.528 6.382 13275 Z= 0.278 Chirality : 0.038 0.144 1454 Planarity : 0.004 0.034 1665 Dihedral : 4.212 22.942 1292 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.61 % Allowed : 22.04 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.25), residues: 1166 helix: 1.52 (0.18), residues: 790 sheet: -0.07 (0.63), residues: 48 loop : -0.31 (0.40), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 106 HIS 0.003 0.001 HIS D 320 PHE 0.026 0.002 PHE C 137 TYR 0.011 0.001 TYR D 109 ARG 0.004 0.000 ARG D 196 *********************** 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 194 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8378 (mtm) cc_final: 0.8135 (mtt) REVERT: A 179 MET cc_start: 0.5664 (pmm) cc_final: 0.5360 (tpp) REVERT: A 268 SER cc_start: 0.8602 (m) cc_final: 0.8322 (p) REVERT: A 342 ILE cc_start: 0.8380 (mm) cc_final: 0.8141 (mt) REVERT: B 122 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.6097 (tp30) REVERT: B 132 GLU cc_start: 0.8315 (tm-30) cc_final: 0.8005 (tp30) REVERT: B 133 LEU cc_start: 0.7632 (tp) cc_final: 0.7232 (tp) REVERT: B 137 PHE cc_start: 0.8218 (m-10) cc_final: 0.7811 (m-80) REVERT: B 155 ASP cc_start: 0.7359 (t0) cc_final: 0.7108 (t0) REVERT: B 179 MET cc_start: 0.5693 (pmm) cc_final: 0.4928 (tpp) REVERT: B 186 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.7032 (ptm160) REVERT: B 234 GLU cc_start: 0.7831 (tp30) cc_final: 0.7513 (mt-10) REVERT: B 342 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8202 (mt) REVERT: C 105 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7570 (tp30) REVERT: C 132 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7964 (tp30) REVERT: C 261 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7792 (mt-10) REVERT: C 266 GLN cc_start: 0.7785 (mt0) cc_final: 0.7409 (mm-40) REVERT: D 342 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8149 (mt) REVERT: D 352 LYS cc_start: 0.8034 (mppt) cc_final: 0.7747 (mptt) outliers start: 36 outliers final: 15 residues processed: 176 average time/residue: 1.0292 time to fit residues: 197.4324 Evaluate side-chains 177 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 A residue 306 SER Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 185 LEU 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 D residue 143 CYS Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 342 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 111 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 D 266 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.178777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.121973 restraints weight = 9725.850| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.81 r_work: 0.3259 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3645 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= 0.189 Angle : 0.538 6.211 13275 Z= 0.282 Chirality : 0.038 0.141 1454 Planarity : 0.004 0.033 1665 Dihedral : 4.111 19.026 1290 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.81 % Allowed : 22.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.25), residues: 1166 helix: 1.55 (0.18), residues: 790 sheet: -0.16 (0.64), residues: 48 loop : -0.27 (0.40), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 145 HIS 0.003 0.001 HIS D 320 PHE 0.029 0.002 PHE A 137 TYR 0.010 0.001 TYR D 109 ARG 0.003 0.000 ARG D 196 *********************** 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 190 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.6797 (ttp-110) cc_final: 0.6550 (ttp80) REVERT: A 128 MET cc_start: 0.8337 (mtm) cc_final: 0.8088 (mtt) REVERT: A 148 ASN cc_start: 0.8330 (t0) cc_final: 0.7982 (t0) REVERT: A 179 MET cc_start: 0.5613 (pmm) cc_final: 0.5342 (tpp) REVERT: A 268 SER cc_start: 0.8592 (m) cc_final: 0.8299 (p) REVERT: A 342 ILE cc_start: 0.8325 (mm) cc_final: 0.8076 (mt) REVERT: B 122 GLU cc_start: 0.6276 (OUTLIER) cc_final: 0.6011 (tp30) REVERT: B 132 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7945 (tp30) REVERT: B 133 LEU cc_start: 0.7566 (tp) cc_final: 0.7162 (tp) REVERT: B 137 PHE cc_start: 0.8206 (m-10) cc_final: 0.7802 (m-80) REVERT: B 155 ASP cc_start: 0.7271 (t0) cc_final: 0.7027 (t0) REVERT: B 179 MET cc_start: 0.5766 (pmm) cc_final: 0.5106 (tpp) REVERT: B 186 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.7022 (ptm160) REVERT: B 234 GLU cc_start: 0.7758 (tp30) cc_final: 0.7416 (mt-10) REVERT: B 342 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8164 (mt) REVERT: C 132 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7895 (tp30) REVERT: C 261 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7780 (mt-10) REVERT: C 266 GLN cc_start: 0.7674 (mt0) cc_final: 0.7377 (mm-40) REVERT: C 342 ILE cc_start: 0.8290 (mm) cc_final: 0.8049 (mt) REVERT: D 209 LYS cc_start: 0.7801 (mttm) cc_final: 0.7360 (mtmm) REVERT: D 342 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8093 (mt) REVERT: D 352 LYS cc_start: 0.7928 (mppt) cc_final: 0.7627 (mptt) outliers start: 28 outliers final: 18 residues processed: 175 average time/residue: 1.0409 time to fit residues: 198.5110 Evaluate side-chains 180 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 A residue 306 SER Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 186 ARG 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 132 GLU Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 252 VAL 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 269 LEU Chi-restraints excluded: chain D residue 342 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 55 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 111 optimal weight: 0.0270 chunk 58 optimal weight: 10.0000 overall best weight: 0.7038 ------------------------------------------------------------------------------- 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 D 266 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.177213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.120551 restraints weight = 9728.147| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.81 r_work: 0.3343 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3728 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= 0.189 Angle : 0.526 6.137 13275 Z= 0.276 Chirality : 0.038 0.140 1454 Planarity : 0.004 0.033 1665 Dihedral : 4.087 18.880 1290 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.61 % Allowed : 23.35 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.25), residues: 1166 helix: 1.58 (0.18), residues: 790 sheet: -0.08 (0.65), residues: 48 loop : -0.29 (0.40), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 145 HIS 0.003 0.001 HIS D 320 PHE 0.024 0.001 PHE C 137 TYR 0.010 0.001 TYR D 109 ARG 0.003 0.000 ARG D 196 *********************** 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 185 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 119 ARG cc_start: 0.6829 (ttp-110) cc_final: 0.6565 (ttp80) REVERT: A 128 MET cc_start: 0.8387 (mtm) cc_final: 0.8135 (mtt) REVERT: A 148 ASN cc_start: 0.8248 (t0) cc_final: 0.7950 (t0) REVERT: A 209 LYS cc_start: 0.7675 (mttm) cc_final: 0.7218 (mtpm) REVERT: A 268 SER cc_start: 0.8530 (m) cc_final: 0.8274 (p) REVERT: A 342 ILE cc_start: 0.8336 (mm) cc_final: 0.8094 (mt) REVERT: B 122 GLU cc_start: 0.6287 (OUTLIER) cc_final: 0.6012 (tp30) REVERT: B 132 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7964 (tp30) REVERT: B 133 LEU cc_start: 0.7602 (tp) cc_final: 0.7173 (tp) REVERT: B 137 PHE cc_start: 0.8245 (m-10) cc_final: 0.7835 (m-80) REVERT: B 155 ASP cc_start: 0.7248 (t0) cc_final: 0.6990 (t0) REVERT: B 179 MET cc_start: 0.5892 (pmm) cc_final: 0.5196 (tpp) REVERT: B 186 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.7019 (ptm160) REVERT: B 209 LYS cc_start: 0.7745 (mtpp) cc_final: 0.7363 (mtpm) REVERT: B 234 GLU cc_start: 0.7726 (tp30) cc_final: 0.7436 (mt-10) REVERT: B 261 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7666 (mt-10) REVERT: B 342 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8191 (mt) REVERT: C 132 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7902 (tp30) REVERT: C 261 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7804 (mt-10) REVERT: C 266 GLN cc_start: 0.7691 (mt0) cc_final: 0.7415 (mm-40) REVERT: C 342 ILE cc_start: 0.8266 (mm) cc_final: 0.8022 (mt) REVERT: D 209 LYS cc_start: 0.7744 (mttm) cc_final: 0.7315 (mtmm) REVERT: D 342 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8128 (mt) REVERT: D 352 LYS cc_start: 0.7929 (mppt) cc_final: 0.7712 (mptt) outliers start: 26 outliers final: 16 residues processed: 175 average time/residue: 1.2457 time to fit residues: 238.0603 Evaluate side-chains 177 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 A residue 269 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 186 ARG 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 132 GLU Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 185 LEU 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 268 SER Chi-restraints excluded: chain D residue 269 LEU 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 107 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 54 optimal weight: 0.0010 chunk 79 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 D 266 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.178926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.131849 restraints weight = 9751.062| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.43 r_work: 0.3357 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3836 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= 0.167 Angle : 0.518 6.211 13275 Z= 0.271 Chirality : 0.037 0.143 1454 Planarity : 0.004 0.031 1665 Dihedral : 4.040 18.596 1290 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.20 % Allowed : 23.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.26), residues: 1166 helix: 1.65 (0.18), residues: 790 sheet: -0.08 (0.66), residues: 48 loop : -0.23 (0.41), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 145 HIS 0.002 0.001 HIS D 320 PHE 0.027 0.001 PHE D 329 TYR 0.009 0.001 TYR D 109 ARG 0.003 0.000 ARG D 196 ********************** 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 189 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.985 Fit side-chains REVERT: A 128 MET cc_start: 0.8454 (mtm) cc_final: 0.8189 (mtt) REVERT: A 148 ASN cc_start: 0.8205 (t0) cc_final: 0.7926 (t0) REVERT: A 209 LYS cc_start: 0.7727 (mttm) cc_final: 0.7318 (mtmm) REVERT: A 268 SER cc_start: 0.8496 (m) cc_final: 0.8281 (p) REVERT: A 342 ILE cc_start: 0.8343 (mm) cc_final: 0.8103 (mt) REVERT: B 132 GLU cc_start: 0.8298 (tm-30) cc_final: 0.8008 (tp30) REVERT: B 133 LEU cc_start: 0.7618 (tp) cc_final: 0.7387 (tp) REVERT: B 137 PHE cc_start: 0.8246 (m-10) cc_final: 0.7884 (m-10) REVERT: B 179 MET cc_start: 0.5836 (pmm) cc_final: 0.5079 (tpp) REVERT: B 209 LYS cc_start: 0.7786 (mtpp) cc_final: 0.7421 (mtpm) REVERT: B 234 GLU cc_start: 0.7828 (tp30) cc_final: 0.7539 (mt-10) REVERT: B 342 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8122 (mt) REVERT: C 209 LYS cc_start: 0.7802 (mttm) cc_final: 0.7378 (mtmm) REVERT: C 261 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7869 (mt-10) REVERT: C 266 GLN cc_start: 0.7773 (mt0) cc_final: 0.7439 (mm-40) REVERT: C 342 ILE cc_start: 0.8394 (mm) cc_final: 0.8181 (mt) REVERT: D 209 LYS cc_start: 0.7761 (mttm) cc_final: 0.7353 (mtmm) REVERT: D 342 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8146 (mt) REVERT: D 352 LYS cc_start: 0.7948 (mppt) cc_final: 0.7740 (mptt) outliers start: 22 outliers final: 14 residues processed: 179 average time/residue: 0.9337 time to fit residues: 182.2601 Evaluate side-chains 174 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 114 TYR 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 185 LEU Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 269 LEU 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 96 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 D 266 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.177245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.125415 restraints weight = 9759.758| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.70 r_work: 0.3273 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9768 Z= 0.204 Angle : 0.545 7.205 13275 Z= 0.287 Chirality : 0.039 0.147 1454 Planarity : 0.004 0.031 1665 Dihedral : 4.075 18.775 1290 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.00 % Allowed : 24.65 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.25), residues: 1166 helix: 1.60 (0.18), residues: 790 sheet: 0.01 (0.68), residues: 48 loop : -0.29 (0.40), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 145 HIS 0.003 0.001 HIS D 237 PHE 0.030 0.002 PHE D 137 TYR 0.010 0.001 TYR A 109 ARG 0.003 0.000 ARG A 189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8172.83 seconds wall clock time: 145 minutes 45.09 seconds (8745.09 seconds total)