Starting phenix.real_space_refine on Mon May 12 22:21:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j7h_36041/05_2025/8j7h_36041.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j7h_36041/05_2025/8j7h_36041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j7h_36041/05_2025/8j7h_36041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j7h_36041/05_2025/8j7h_36041.map" model { file = "/net/cci-nas-00/data/ceres_data/8j7h_36041/05_2025/8j7h_36041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j7h_36041/05_2025/8j7h_36041.cif" } resolution = 3.3 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= -0.000 sd= 0.079 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 49 5.16 5 C 6228 2.51 5 N 1506 2.21 5 O 1674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9457 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2329 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 282} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2327 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 282} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2328 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 282} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2319 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 282} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 153 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.93, per 1000 atoms: 0.63 Number of scatterers: 9457 At special positions: 0 Unit cell: (126.88, 125.84, 93.6, 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 49 16.00 O 1674 8.00 N 1506 7.00 C 6228 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: 2.50 Conformation dependent library (CDL) restraints added in 1.1 seconds 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 4 sheets defined 78.2% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.919A 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 139 removed outlier: 3.917A pdb=" N TRP A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 172 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 185 through 191 removed outlier: 4.152A pdb=" N ILE A 190 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 removed outlier: 3.792A 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: 4.424A pdb=" N ASN A 216 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 258 through 265 removed outlier: 3.653A pdb=" N VAL A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 288 Processing helix chain 'A' and resid 290 through 304 Processing helix chain 'A' and resid 311 through 319 removed outlier: 4.389A pdb=" N ALA A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 3.633A 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 337 through 358 removed outlier: 3.505A pdb=" N ASP A 358 " --> pdb=" O VAL A 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 removed outlier: 3.920A pdb=" N VAL B 76 " --> pdb=" O HIS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 107 Processing helix chain 'B' and resid 114 through 139 removed outlier: 3.917A pdb=" N TRP B 118 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 172 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 185 through 191 removed outlier: 4.153A pdb=" N ILE B 190 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 removed outlier: 3.791A 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: 4.424A pdb=" N ASN B 216 " --> pdb=" O PRO B 212 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 258 through 265 removed outlier: 3.654A pdb=" N VAL B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 288 Processing helix chain 'B' and resid 290 through 304 Processing helix chain 'B' and resid 311 through 319 removed outlier: 4.390A pdb=" N ALA B 315 " --> pdb=" O VAL B 311 " (cutoff:3.500A) removed outlier: 3.633A 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 337 through 358 removed outlier: 3.505A pdb=" N ASP B 358 " --> pdb=" O VAL B 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.920A pdb=" N VAL C 76 " --> pdb=" O HIS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 107 Processing helix chain 'C' and resid 114 through 139 removed outlier: 3.918A pdb=" N TRP C 118 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 172 Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 185 through 191 removed outlier: 4.153A pdb=" N ILE C 190 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 removed outlier: 3.792A 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: 4.423A pdb=" N ASN C 216 " --> pdb=" O PRO C 212 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA C 217 " --> pdb=" O GLY C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 265 removed outlier: 3.654A pdb=" N VAL C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU C 263 " --> pdb=" O GLY C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 288 Processing helix chain 'C' and resid 290 through 304 Processing helix chain 'C' and resid 311 through 319 removed outlier: 4.390A pdb=" N ALA C 315 " --> pdb=" O VAL C 311 " (cutoff:3.500A) removed outlier: 3.633A 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 337 through 358 removed outlier: 3.504A pdb=" N ASP C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 81 removed outlier: 3.920A 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 139 removed outlier: 3.917A pdb=" N TRP D 118 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY D 139 " --> pdb=" O ILE D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 172 Processing helix chain 'D' and resid 179 through 184 Processing helix chain 'D' and resid 185 through 191 removed outlier: 4.153A pdb=" N ILE D 190 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 removed outlier: 3.792A 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: 4.423A pdb=" N ASN D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA D 217 " --> pdb=" O GLY D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 265 removed outlier: 3.654A pdb=" N VAL D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU D 263 " --> pdb=" O GLY D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 288 Processing helix chain 'D' and resid 290 through 304 Processing helix chain 'D' and resid 311 through 319 removed outlier: 4.390A pdb=" N ALA D 315 " --> pdb=" O VAL D 311 " (cutoff:3.500A) removed outlier: 3.633A 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 337 through 358 removed outlier: 3.504A pdb=" N ASP D 358 " --> pdb=" O VAL D 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 21 removed outlier: 3.619A pdb=" N LYS E 12 " --> pdb=" O ALA E 8 " (cutoff:3.500A) 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 248 646 hydrogen bonds defined for protein. 1902 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: 2.64 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1491 1.32 - 1.44: 2951 1.44 - 1.56: 5195 1.56 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 9711 Sorted by residual: bond pdb=" C LEU C 156 " pdb=" O LEU C 156 " ideal model delta sigma weight residual 1.236 1.198 0.038 1.15e-02 7.56e+03 1.10e+01 bond pdb=" C LEU B 156 " pdb=" O LEU B 156 " ideal model delta sigma weight residual 1.236 1.199 0.038 1.15e-02 7.56e+03 1.06e+01 bond pdb=" C LEU A 156 " pdb=" O LEU A 156 " ideal model delta sigma weight residual 1.236 1.206 0.031 1.15e-02 7.56e+03 7.05e+00 bond pdb=" C VAL B 159 " pdb=" O VAL B 159 " ideal model delta sigma weight residual 1.237 1.208 0.030 1.23e-02 6.61e+03 5.80e+00 bond pdb=" C VAL C 159 " pdb=" O VAL C 159 " ideal model delta sigma weight residual 1.237 1.208 0.029 1.29e-02 6.01e+03 5.06e+00 ... (remaining 9706 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 12970 2.14 - 4.28: 188 4.28 - 6.42: 34 6.42 - 8.56: 9 8.56 - 10.70: 7 Bond angle restraints: 13208 Sorted by residual: angle pdb=" N ASN B 251 " pdb=" CA ASN B 251 " pdb=" C ASN B 251 " ideal model delta sigma weight residual 111.07 118.17 -7.10 1.07e+00 8.73e-01 4.40e+01 angle pdb=" N ASN D 270 " pdb=" CA ASN D 270 " pdb=" C ASN D 270 " ideal model delta sigma weight residual 107.48 118.18 -10.70 2.29e+00 1.91e-01 2.18e+01 angle pdb=" N SER A 274 " pdb=" CA SER A 274 " pdb=" C SER A 274 " ideal model delta sigma weight residual 110.24 116.43 -6.19 1.41e+00 5.03e-01 1.93e+01 angle pdb=" N ASN B 270 " pdb=" CA ASN B 270 " pdb=" C ASN B 270 " ideal model delta sigma weight residual 107.48 117.47 -9.99 2.29e+00 1.91e-01 1.90e+01 angle pdb=" N LEU A 269 " pdb=" CA LEU A 269 " pdb=" C LEU A 269 " ideal model delta sigma weight residual 112.97 108.41 4.56 1.06e+00 8.90e-01 1.85e+01 ... (remaining 13203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 5040 17.31 - 34.63: 369 34.63 - 51.94: 89 51.94 - 69.26: 18 69.26 - 86.57: 4 Dihedral angle restraints: 5520 sinusoidal: 2077 harmonic: 3443 Sorted by residual: dihedral pdb=" CD ARG E 10 " pdb=" NE ARG E 10 " pdb=" CZ ARG E 10 " pdb=" NH1 ARG E 10 " ideal model delta sinusoidal sigma weight residual 0.00 31.73 -31.73 1 1.00e+01 1.00e-02 1.43e+01 dihedral pdb=" C VAL D 158 " pdb=" N VAL D 158 " pdb=" CA VAL D 158 " pdb=" CB VAL D 158 " ideal model delta harmonic sigma weight residual -122.00 -131.30 9.30 0 2.50e+00 1.60e-01 1.38e+01 dihedral pdb=" CA PHE A 235 " pdb=" C PHE A 235 " pdb=" N TYR A 236 " pdb=" CA TYR A 236 " ideal model delta harmonic sigma weight residual -180.00 -162.53 -17.47 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 5517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1103 0.049 - 0.098: 293 0.098 - 0.147: 30 0.147 - 0.196: 23 0.196 - 0.245: 13 Chirality restraints: 1462 Sorted by residual: chirality pdb=" CA VAL D 158 " pdb=" N VAL D 158 " pdb=" C VAL D 158 " pdb=" CB VAL D 158 " both_signs ideal model delta sigma weight residual False 2.44 2.20 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA VAL A 158 " pdb=" N VAL A 158 " pdb=" C VAL A 158 " pdb=" CB VAL A 158 " both_signs ideal model delta sigma weight residual False 2.44 2.22 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA SER C 274 " pdb=" N SER C 274 " pdb=" C SER C 274 " pdb=" CB SER C 274 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1459 not shown) Planarity restraints: 1656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 10 " 0.623 9.50e-02 1.11e+02 2.80e-01 4.95e+01 pdb=" NE ARG E 10 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG E 10 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG E 10 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 10 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 137 " -0.010 2.00e-02 2.50e+03 2.06e-02 7.43e+00 pdb=" CG PHE A 137 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A 137 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE A 137 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 137 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 137 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE A 137 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 137 " -0.010 2.00e-02 2.50e+03 2.05e-02 7.38e+00 pdb=" CG PHE B 137 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE B 137 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE B 137 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE B 137 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE B 137 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE B 137 " 0.006 2.00e-02 2.50e+03 ... (remaining 1653 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1911 2.77 - 3.30: 9786 3.30 - 3.83: 16389 3.83 - 4.37: 19362 4.37 - 4.90: 32013 Nonbonded interactions: 79461 Sorted by model distance: nonbonded pdb=" O GLU B 122 " pdb=" ND2 ASN B 126 " model vdw 2.232 3.120 nonbonded pdb=" O GLU D 122 " pdb=" ND2 ASN D 126 " model vdw 2.232 3.120 nonbonded pdb=" O GLU A 122 " pdb=" ND2 ASN A 126 " model vdw 2.232 3.120 nonbonded pdb=" O GLU C 122 " pdb=" ND2 ASN C 126 " model vdw 2.232 3.120 nonbonded pdb=" OH TYR A 283 " pdb=" O VAL A 311 " model vdw 2.242 3.040 ... (remaining 79456 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' and (resid 69 through 71 or (resid 72 and (name N or name CA or name \ C or name O or name CB )) or resid 73 through 175 or (resid 176 through 180 and \ (name N or name CA or name C or name O or name CB )) or resid 181 through 358)) selection = (chain 'B' and (resid 69 through 174 or (resid 175 through 180 and (name N or na \ me CA or name C or name O or name CB )) or resid 181 through 358)) selection = (chain 'C' and (resid 69 through 71 or (resid 72 and (name N or name CA or name \ C or name O or name CB )) or resid 73 through 74 or (resid 75 and (name N or nam \ e CA or name C or name O or name CB )) or resid 76 through 358)) 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.710 Find NCS groups from input model: 0.340 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: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9711 Z= 0.201 Angle : 0.746 10.696 13208 Z= 0.440 Chirality : 0.049 0.245 1462 Planarity : 0.008 0.280 1656 Dihedral : 13.739 86.573 3320 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.10 % Allowed : 3.48 % Favored : 96.42 % 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: 0.52 (0.25), residues: 1170 helix: 0.99 (0.19), residues: 765 sheet: -0.03 (0.71), residues: 48 loop : -0.89 (0.37), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 145 HIS 0.006 0.002 HIS E 6 PHE 0.043 0.001 PHE A 137 TYR 0.012 0.002 TYR D 80 ARG 0.023 0.001 ARG E 10 Details of bonding type rmsd hydrogen bonds : bond 0.13348 ( 646) hydrogen bonds : angle 6.24992 ( 1902) covalent geometry : bond 0.00364 ( 9711) covalent geometry : angle 0.74557 (13208) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 ASN cc_start: 0.7374 (m110) cc_final: 0.7128 (m110) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.2081 time to fit residues: 65.1412 Evaluate side-chains 187 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 92 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN C 136 ASN D 343 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.203768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.163848 restraints weight = 9471.176| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.68 r_work: 0.3593 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9711 Z= 0.134 Angle : 0.543 7.641 13208 Z= 0.294 Chirality : 0.040 0.183 1462 Planarity : 0.004 0.041 1656 Dihedral : 4.321 14.877 1294 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.51 % Allowed : 6.44 % Favored : 93.05 % 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: 0.50 (0.25), residues: 1170 helix: 0.95 (0.18), residues: 782 sheet: -0.40 (0.60), residues: 48 loop : -0.88 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 307 HIS 0.008 0.002 HIS C 237 PHE 0.022 0.001 PHE A 144 TYR 0.011 0.001 TYR D 236 ARG 0.007 0.000 ARG E 9 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 646) hydrogen bonds : angle 5.31398 ( 1902) covalent geometry : bond 0.00284 ( 9711) covalent geometry : angle 0.54302 (13208) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 205 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 ASN cc_start: 0.8904 (m-40) cc_final: 0.8649 (m-40) REVERT: A 209 LYS cc_start: 0.7930 (mtpt) cc_final: 0.7670 (mtpp) REVERT: B 130 LEU cc_start: 0.8831 (tp) cc_final: 0.8621 (tt) outliers start: 5 outliers final: 3 residues processed: 208 average time/residue: 0.2079 time to fit residues: 60.4580 Evaluate side-chains 183 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 180 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain D residue 277 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 82 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 104 optimal weight: 0.0970 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN B 126 ASN C 126 ASN C 152 ASN D 126 ASN D 152 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.200399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.158642 restraints weight = 9613.419| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.65 r_work: 0.3578 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9711 Z= 0.141 Angle : 0.514 7.644 13208 Z= 0.278 Chirality : 0.039 0.162 1462 Planarity : 0.004 0.067 1656 Dihedral : 4.238 17.205 1294 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.72 % Allowed : 8.38 % Favored : 90.90 % 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: 0.52 (0.25), residues: 1170 helix: 0.93 (0.18), residues: 814 sheet: -0.65 (0.56), residues: 48 loop : -0.87 (0.39), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 307 HIS 0.009 0.002 HIS E 6 PHE 0.026 0.001 PHE D 144 TYR 0.015 0.001 TYR D 288 ARG 0.009 0.000 ARG E 9 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 646) hydrogen bonds : angle 5.28636 ( 1902) covalent geometry : bond 0.00314 ( 9711) covalent geometry : angle 0.51400 (13208) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 187 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 LYS cc_start: 0.8016 (mtpt) cc_final: 0.7766 (mtpp) REVERT: D 209 LYS cc_start: 0.7995 (mtpt) cc_final: 0.7758 (mtpp) outliers start: 7 outliers final: 6 residues processed: 189 average time/residue: 0.2172 time to fit residues: 56.9507 Evaluate side-chains 183 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 177 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 322 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 116 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 ASN B 126 ASN B 152 ASN ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN C 136 ASN D 126 ASN ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.194713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.152732 restraints weight = 9714.760| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.78 r_work: 0.3447 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9711 Z= 0.165 Angle : 0.538 8.408 13208 Z= 0.288 Chirality : 0.040 0.147 1462 Planarity : 0.004 0.041 1656 Dihedral : 4.231 16.495 1294 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.43 % Allowed : 10.12 % Favored : 88.45 % 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: 0.38 (0.24), residues: 1170 helix: 0.84 (0.18), residues: 814 sheet: -0.71 (0.52), residues: 48 loop : -0.98 (0.39), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 145 HIS 0.007 0.002 HIS A 320 PHE 0.027 0.001 PHE D 144 TYR 0.017 0.002 TYR A 288 ARG 0.010 0.001 ARG E 9 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 646) hydrogen bonds : angle 5.37568 ( 1902) covalent geometry : bond 0.00385 ( 9711) covalent geometry : angle 0.53804 (13208) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASN cc_start: 0.8712 (m-40) cc_final: 0.8414 (m-40) REVERT: A 156 LEU cc_start: 0.8891 (tp) cc_final: 0.8662 (mt) REVERT: A 185 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7519 (tt) REVERT: B 195 LYS cc_start: 0.7733 (tttt) cc_final: 0.7520 (tttt) outliers start: 14 outliers final: 7 residues processed: 202 average time/residue: 0.2031 time to fit residues: 57.8749 Evaluate side-chains 187 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 179 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 322 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 48 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 62 optimal weight: 0.0870 chunk 35 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 126 ASN B 126 ASN B 343 ASN C 96 ASN C 126 ASN C 136 ASN D 126 ASN ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.197103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.156236 restraints weight = 9671.881| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.71 r_work: 0.3488 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9711 Z= 0.131 Angle : 0.513 7.150 13208 Z= 0.272 Chirality : 0.038 0.138 1462 Planarity : 0.004 0.039 1656 Dihedral : 4.114 17.781 1294 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.92 % Allowed : 12.27 % Favored : 86.81 % 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: 0.58 (0.25), residues: 1170 helix: 1.02 (0.18), residues: 818 sheet: -0.89 (0.49), residues: 48 loop : -0.99 (0.39), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 307 HIS 0.006 0.002 HIS A 237 PHE 0.024 0.001 PHE B 144 TYR 0.012 0.001 TYR C 80 ARG 0.008 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 646) hydrogen bonds : angle 5.27740 ( 1902) covalent geometry : bond 0.00289 ( 9711) covalent geometry : angle 0.51269 (13208) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 192 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASN cc_start: 0.8663 (m-40) cc_final: 0.8359 (m110) REVERT: A 185 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7589 (tt) REVERT: C 136 ASN cc_start: 0.7875 (m110) cc_final: 0.7645 (m110) outliers start: 9 outliers final: 6 residues processed: 194 average time/residue: 0.2237 time to fit residues: 60.2895 Evaluate side-chains 183 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 176 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 322 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 3 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 18 optimal weight: 0.0030 chunk 6 optimal weight: 3.9990 chunk 64 optimal weight: 0.1980 chunk 78 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 83 optimal weight: 0.1980 chunk 112 optimal weight: 0.4980 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN B 126 ASN D 126 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.199201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.157174 restraints weight = 9632.816| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.61 r_work: 0.3521 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9711 Z= 0.116 Angle : 0.480 6.412 13208 Z= 0.261 Chirality : 0.038 0.138 1462 Planarity : 0.004 0.032 1656 Dihedral : 4.028 17.341 1294 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.92 % Allowed : 13.19 % Favored : 85.89 % 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: 0.48 (0.25), residues: 1170 helix: 0.85 (0.18), residues: 854 sheet: -0.93 (0.48), residues: 48 loop : -0.92 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 307 HIS 0.006 0.001 HIS D 237 PHE 0.027 0.001 PHE D 144 TYR 0.009 0.001 TYR C 80 ARG 0.006 0.000 ARG B 196 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 646) hydrogen bonds : angle 5.17985 ( 1902) covalent geometry : bond 0.00242 ( 9711) covalent geometry : angle 0.47959 (13208) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 194 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 LEU cc_start: 0.8037 (tp) cc_final: 0.7621 (tt) REVERT: B 209 LYS cc_start: 0.7992 (mtpt) cc_final: 0.7720 (mtpp) outliers start: 9 outliers final: 4 residues processed: 197 average time/residue: 0.1993 time to fit residues: 55.2460 Evaluate side-chains 184 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 180 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 322 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 14 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 33 optimal weight: 0.0570 chunk 57 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN A 152 ASN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN C 126 ASN C 136 ASN D 126 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.192213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.150463 restraints weight = 9862.286| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.84 r_work: 0.3489 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9711 Z= 0.143 Angle : 0.512 9.635 13208 Z= 0.278 Chirality : 0.039 0.148 1462 Planarity : 0.004 0.032 1656 Dihedral : 4.069 15.112 1294 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.23 % Allowed : 13.50 % Favored : 85.28 % 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: 0.43 (0.24), residues: 1170 helix: 0.83 (0.18), residues: 842 sheet: -0.75 (0.49), residues: 48 loop : -0.94 (0.40), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 307 HIS 0.005 0.001 HIS D 237 PHE 0.024 0.001 PHE B 144 TYR 0.015 0.001 TYR C 80 ARG 0.006 0.000 ARG B 196 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 646) hydrogen bonds : angle 5.26303 ( 1902) covalent geometry : bond 0.00327 ( 9711) covalent geometry : angle 0.51180 (13208) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7577 (tt) REVERT: A 343 ASN cc_start: 0.8489 (m110) cc_final: 0.8110 (m110) REVERT: B 209 LYS cc_start: 0.8009 (mtpt) cc_final: 0.7743 (mtpp) REVERT: D 195 LYS cc_start: 0.7417 (tttt) cc_final: 0.7197 (ttpt) outliers start: 12 outliers final: 7 residues processed: 191 average time/residue: 0.1947 time to fit residues: 52.6520 Evaluate side-chains 187 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 179 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 322 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 12 optimal weight: 0.4980 chunk 46 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 111 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN C 126 ASN C 136 ASN D 126 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.196738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.157920 restraints weight = 9754.728| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.44 r_work: 0.3575 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9711 Z= 0.134 Angle : 0.493 5.638 13208 Z= 0.272 Chirality : 0.038 0.146 1462 Planarity : 0.004 0.037 1656 Dihedral : 4.083 15.053 1294 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.43 % Allowed : 13.39 % Favored : 85.17 % 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: 0.48 (0.24), residues: 1170 helix: 0.85 (0.17), residues: 846 sheet: -0.74 (0.49), residues: 48 loop : -0.92 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 307 HIS 0.004 0.001 HIS C 237 PHE 0.026 0.001 PHE B 144 TYR 0.016 0.001 TYR C 80 ARG 0.010 0.000 ARG B 196 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 646) hydrogen bonds : angle 5.26851 ( 1902) covalent geometry : bond 0.00300 ( 9711) covalent geometry : angle 0.49259 (13208) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.8383 (m-30) cc_final: 0.8092 (m-30) REVERT: A 185 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7715 (tt) REVERT: A 343 ASN cc_start: 0.8371 (m110) cc_final: 0.8060 (m110) REVERT: B 209 LYS cc_start: 0.8022 (mtpt) cc_final: 0.7781 (mtpp) REVERT: C 250 ASP cc_start: 0.7635 (t0) cc_final: 0.7118 (t0) outliers start: 14 outliers final: 9 residues processed: 190 average time/residue: 0.1931 time to fit residues: 52.2148 Evaluate side-chains 190 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 322 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 69 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN C 126 ASN D 126 ASN E 6 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.189534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.148964 restraints weight = 9845.956| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 1.77 r_work: 0.3484 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9711 Z= 0.168 Angle : 0.546 9.958 13208 Z= 0.298 Chirality : 0.040 0.149 1462 Planarity : 0.004 0.048 1656 Dihedral : 4.168 14.836 1294 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.64 % Allowed : 13.91 % Favored : 84.46 % 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: 0.41 (0.24), residues: 1170 helix: 0.76 (0.17), residues: 846 sheet: -0.69 (0.50), residues: 48 loop : -0.81 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 307 HIS 0.004 0.001 HIS C 237 PHE 0.024 0.001 PHE B 144 TYR 0.013 0.002 TYR C 80 ARG 0.009 0.001 ARG B 196 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 646) hydrogen bonds : angle 5.38149 ( 1902) covalent geometry : bond 0.00396 ( 9711) covalent geometry : angle 0.54587 (13208) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7642 (tt) REVERT: A 238 MET cc_start: 0.8052 (tpp) cc_final: 0.7052 (tpp) REVERT: A 343 ASN cc_start: 0.8489 (m110) cc_final: 0.8096 (m110) REVERT: B 196 ARG cc_start: 0.7431 (mmt90) cc_final: 0.7185 (mmt90) REVERT: B 209 LYS cc_start: 0.8038 (mtpt) cc_final: 0.7792 (mtpp) REVERT: D 195 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.7085 (ttpt) outliers start: 16 outliers final: 11 residues processed: 183 average time/residue: 0.1970 time to fit residues: 51.0752 Evaluate side-chains 180 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 322 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 76 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 39 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 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 126 ASN B 126 ASN C 126 ASN C 136 ASN D 126 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.195321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.156417 restraints weight = 9824.848| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 1.43 r_work: 0.3552 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9711 Z= 0.144 Angle : 0.519 6.549 13208 Z= 0.283 Chirality : 0.039 0.149 1462 Planarity : 0.004 0.030 1656 Dihedral : 4.142 15.171 1294 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.43 % Allowed : 14.72 % Favored : 83.84 % 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: 0.47 (0.24), residues: 1170 helix: 0.81 (0.17), residues: 846 sheet: -0.60 (0.52), residues: 48 loop : -0.84 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 307 HIS 0.004 0.001 HIS D 237 PHE 0.024 0.001 PHE D 144 TYR 0.019 0.001 TYR C 80 ARG 0.009 0.000 ARG B 196 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 646) hydrogen bonds : angle 5.33492 ( 1902) covalent geometry : bond 0.00331 ( 9711) covalent geometry : angle 0.51881 (13208) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 183 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7684 (tt) REVERT: A 318 GLU cc_start: 0.7200 (tp30) cc_final: 0.6902 (tp30) REVERT: A 343 ASN cc_start: 0.8399 (m110) cc_final: 0.8199 (m-40) REVERT: B 209 LYS cc_start: 0.8020 (mtpt) cc_final: 0.7797 (mtpp) outliers start: 14 outliers final: 10 residues processed: 188 average time/residue: 0.1982 time to fit residues: 53.2211 Evaluate side-chains 188 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 177 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 322 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 103 optimal weight: 0.6980 chunk 72 optimal weight: 0.0770 chunk 96 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 10 optimal weight: 0.0980 chunk 117 optimal weight: 0.0980 chunk 57 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN C 126 ASN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.198870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.157923 restraints weight = 9607.315| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.79 r_work: 0.3547 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9711 Z= 0.121 Angle : 0.517 10.108 13208 Z= 0.278 Chirality : 0.038 0.148 1462 Planarity : 0.004 0.038 1656 Dihedral : 4.107 16.782 1294 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.02 % Allowed : 15.64 % Favored : 83.33 % 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: 0.59 (0.25), residues: 1170 helix: 0.89 (0.18), residues: 850 sheet: -0.57 (0.52), residues: 48 loop : -0.76 (0.42), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 307 HIS 0.005 0.002 HIS D 237 PHE 0.023 0.001 PHE D 144 TYR 0.021 0.001 TYR C 80 ARG 0.007 0.000 ARG E 10 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 646) hydrogen bonds : angle 5.22128 ( 1902) covalent geometry : bond 0.00258 ( 9711) covalent geometry : angle 0.51713 (13208) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5295.07 seconds wall clock time: 92 minutes 36.92 seconds (5556.92 seconds total)