Starting phenix.real_space_refine on Sat Aug 23 03:46:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v8i_31802/08_2025/7v8i_31802_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v8i_31802/08_2025/7v8i_31802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v8i_31802/08_2025/7v8i_31802_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v8i_31802/08_2025/7v8i_31802_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v8i_31802/08_2025/7v8i_31802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v8i_31802/08_2025/7v8i_31802.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 5956 2.51 5 N 1651 2.21 5 O 1726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9388 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 2841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2841 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 21, 'TRANS': 374} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 8, 'HIS:plan': 1, 'ASP:plan': 4, 'ARG:plan': 7, 'GLN:plan1': 3, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "D" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1751 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 220} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 2978 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 14, 'TRANS': 392} Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 6, 'ASP:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 5, 'ASN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 101 Chain: "F" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1754 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.35, per 1000 atoms: 0.25 Number of scatterers: 9388 At special positions: 0 Unit cell: (95, 86, 159, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 6 15.00 Mg 2 11.99 O 1726 8.00 N 1651 7.00 C 5956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 343.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2308 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 9 sheets defined 48.8% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'C' and resid 7 through 16 Processing helix chain 'C' and resid 22 through 28 Processing helix chain 'C' and resid 28 through 59 removed outlier: 3.764A pdb=" N ILE C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 148 through 155 Processing helix chain 'C' and resid 195 through 198 removed outlier: 3.549A pdb=" N GLY C 198 " --> pdb=" O GLU C 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 195 through 198' Processing helix chain 'C' and resid 205 through 212 Processing helix chain 'C' and resid 233 through 237 removed outlier: 3.824A pdb=" N SER C 236 " --> pdb=" O ASP C 233 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN C 237 " --> pdb=" O SER C 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 233 through 237' Processing helix chain 'C' and resid 254 through 293 removed outlier: 3.816A pdb=" N GLN C 258 " --> pdb=" O GLY C 254 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER C 285 " --> pdb=" O ASN C 281 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU C 286 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS C 293 " --> pdb=" O MET C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 303 Processing helix chain 'C' and resid 306 through 335 Processing helix chain 'C' and resid 340 through 344 Processing helix chain 'C' and resid 361 through 379 Processing helix chain 'C' and resid 381 through 390 Processing helix chain 'D' and resid 48 through 56 Processing helix chain 'D' and resid 77 through 88 Processing helix chain 'D' and resid 103 through 115 Proline residue: D 111 - end of helix Processing helix chain 'D' and resid 118 through 134 removed outlier: 3.744A pdb=" N SER D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 147 through 161 Processing helix chain 'D' and resid 177 through 195 Processing helix chain 'D' and resid 205 through 211 Processing helix chain 'E' and resid 11 through 17 removed outlier: 4.169A pdb=" N ARG E 15 " --> pdb=" O LEU E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 60 removed outlier: 3.601A pdb=" N LEU E 60 " --> pdb=" O ASN E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 87 removed outlier: 4.254A pdb=" N ALA E 81 " --> pdb=" O ASN E 77 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS E 87 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 127 Processing helix chain 'E' and resid 128 through 133 removed outlier: 3.657A pdb=" N VAL E 133 " --> pdb=" O LEU E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 142 Processing helix chain 'E' and resid 151 through 159 removed outlier: 5.161A pdb=" N ALA E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 201 removed outlier: 3.536A pdb=" N HIS E 201 " --> pdb=" O GLN E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 215 Processing helix chain 'E' and resid 233 through 243 Processing helix chain 'E' and resid 258 through 294 removed outlier: 4.044A pdb=" N LEU E 278 " --> pdb=" O LEU E 274 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 305 Processing helix chain 'E' and resid 313 through 344 removed outlier: 3.879A pdb=" N GLN E 344 " --> pdb=" O VAL E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 353 removed outlier: 4.552A pdb=" N ILE E 352 " --> pdb=" O ILE E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 356 No H-bonds generated for 'chain 'E' and resid 354 through 356' Processing helix chain 'E' and resid 376 through 405 Proline residue: E 398 - end of helix removed outlier: 3.593A pdb=" N ILE E 405 " --> pdb=" O ARG E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 410 Processing helix chain 'F' and resid 48 through 56 Processing helix chain 'F' and resid 77 through 88 Processing helix chain 'F' and resid 103 through 115 Proline residue: F 111 - end of helix Processing helix chain 'F' and resid 118 through 134 Processing helix chain 'F' and resid 142 through 146 Processing helix chain 'F' and resid 147 through 162 removed outlier: 4.798A pdb=" N ASN F 162 " --> pdb=" O ARG F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 194 Processing helix chain 'F' and resid 205 through 211 Processing sheet with id=AA1, first strand: chain 'C' and resid 176 through 185 removed outlier: 11.767A pdb=" N GLY C 176 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 9.878A pdb=" N SER C 170 " --> pdb=" O GLY C 176 " (cutoff:3.500A) removed outlier: 9.671A pdb=" N ILE C 178 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N SER C 168 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER C 180 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 9.748A pdb=" N ASP C 100 " --> pdb=" O PRO C 167 " (cutoff:3.500A) removed outlier: 11.076A pdb=" N ALA C 169 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 15.544A pdb=" N THR C 98 " --> pdb=" O ALA C 169 " (cutoff:3.500A) removed outlier: 22.573A pdb=" N GLN C 171 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 27.579A pdb=" N ILE C 96 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 35.076A pdb=" N THR C 173 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 39.560A pdb=" N ALA C 94 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N MET C 201 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL C 113 " --> pdb=" O MET C 201 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL C 203 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU C 115 " --> pdb=" O VAL C 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 176 through 185 removed outlier: 11.767A pdb=" N GLY C 176 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 9.878A pdb=" N SER C 170 " --> pdb=" O GLY C 176 " (cutoff:3.500A) removed outlier: 9.671A pdb=" N ILE C 178 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N SER C 168 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER C 180 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 9.748A pdb=" N ASP C 100 " --> pdb=" O PRO C 167 " (cutoff:3.500A) removed outlier: 11.076A pdb=" N ALA C 169 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 15.544A pdb=" N THR C 98 " --> pdb=" O ALA C 169 " (cutoff:3.500A) removed outlier: 22.573A pdb=" N GLN C 171 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 27.579A pdb=" N ILE C 96 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 35.076A pdb=" N THR C 173 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 39.560A pdb=" N ALA C 94 " --> pdb=" O THR C 173 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 129 through 130 removed outlier: 4.188A pdb=" N VAL C 130 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N THR C 189 " --> pdb=" O VAL C 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 25 through 32 removed outlier: 7.029A pdb=" N HIS D 26 " --> pdb=" O CYS D 12 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N CYS D 12 " --> pdb=" O HIS D 26 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL D 28 " --> pdb=" O ASN D 10 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN D 10 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU D 11 " --> pdb=" O SER D 63 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER D 63 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 89 through 92 removed outlier: 6.439A pdb=" N VAL D 167 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N VAL D 202 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA D 169 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N GLN D 215 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLU D 226 " --> pdb=" O GLN D 215 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLU D 217 " --> pdb=" O THR D 224 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 109 through 117 Processing sheet with id=AA7, first strand: chain 'E' and resid 165 through 169 Processing sheet with id=AA8, first strand: chain 'F' and resid 22 through 32 removed outlier: 6.513A pdb=" N ASP F 23 " --> pdb=" O TYR F 15 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N TYR F 15 " --> pdb=" O ASP F 23 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU F 11 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N SER F 29 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASP F 9 " --> pdb=" O SER F 29 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N SER F 31 " --> pdb=" O GLN F 7 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN F 7 " --> pdb=" O SER F 31 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU F 11 " --> pdb=" O SER F 63 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N SER F 63 " --> pdb=" O LEU F 11 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 89 through 92 removed outlier: 6.179A pdb=" N VAL F 167 " --> pdb=" O LEU F 200 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL F 202 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA F 169 " --> pdb=" O VAL F 202 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLN F 215 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU F 226 " --> pdb=" O GLN F 215 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLU F 217 " --> pdb=" O THR F 224 " (cutoff:3.500A) 512 hydrogen bonds defined for protein. 1458 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1901 1.33 - 1.45: 2032 1.45 - 1.57: 5510 1.57 - 1.69: 9 1.69 - 1.82: 90 Bond restraints: 9542 Sorted by residual: bond pdb=" O3A ANP F 302 " pdb=" PB ANP F 302 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.34e+01 bond pdb=" O3A ANP D 302 " pdb=" PB ANP D 302 " ideal model delta sigma weight residual 1.700 1.585 0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" N3B ANP F 302 " pdb=" PG ANP F 302 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C4 ANP D 302 " pdb=" C5 ANP D 302 " ideal model delta sigma weight residual 1.387 1.469 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" O5' ANP F 302 " pdb=" PA ANP F 302 " ideal model delta sigma weight residual 1.655 1.578 0.077 2.00e-02 2.50e+03 1.49e+01 ... (remaining 9537 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.49: 12864 3.49 - 6.99: 93 6.99 - 10.48: 20 10.48 - 13.98: 3 13.98 - 17.47: 2 Bond angle restraints: 12982 Sorted by residual: angle pdb=" N ARG E 306 " pdb=" CA ARG E 306 " pdb=" C ARG E 306 " ideal model delta sigma weight residual 110.41 119.15 -8.74 1.23e+00 6.61e-01 5.05e+01 angle pdb=" N GLY F 18 " pdb=" CA GLY F 18 " pdb=" C GLY F 18 " ideal model delta sigma weight residual 111.36 119.66 -8.30 1.17e+00 7.31e-01 5.03e+01 angle pdb=" N VAL C 349 " pdb=" CA VAL C 349 " pdb=" C VAL C 349 " ideal model delta sigma weight residual 113.10 106.98 6.12 9.70e-01 1.06e+00 3.98e+01 angle pdb=" PB ANP F 302 " pdb=" N3B ANP F 302 " pdb=" PG ANP F 302 " ideal model delta sigma weight residual 126.95 109.48 17.47 3.00e+00 1.11e-01 3.39e+01 angle pdb=" PB ANP D 302 " pdb=" N3B ANP D 302 " pdb=" PG ANP D 302 " ideal model delta sigma weight residual 126.95 110.77 16.18 3.00e+00 1.11e-01 2.91e+01 ... (remaining 12977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 5608 35.39 - 70.79: 144 70.79 - 106.18: 18 106.18 - 141.57: 0 141.57 - 176.96: 2 Dihedral angle restraints: 5772 sinusoidal: 2186 harmonic: 3586 Sorted by residual: dihedral pdb=" O1A ANP D 302 " pdb=" O3A ANP D 302 " pdb=" PA ANP D 302 " pdb=" PB ANP D 302 " ideal model delta sinusoidal sigma weight residual 83.11 -93.85 176.96 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A ANP F 302 " pdb=" O3A ANP F 302 " pdb=" PA ANP F 302 " pdb=" PB ANP F 302 " ideal model delta sinusoidal sigma weight residual 83.11 -72.13 155.24 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" CA MET D 37 " pdb=" C MET D 37 " pdb=" N MET D 38 " pdb=" CA MET D 38 " ideal model delta harmonic sigma weight residual -180.00 -160.86 -19.14 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 5769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1306 0.065 - 0.131: 223 0.131 - 0.196: 9 0.196 - 0.262: 5 0.262 - 0.327: 4 Chirality restraints: 1547 Sorted by residual: chirality pdb=" CA PRO E 74 " pdb=" N PRO E 74 " pdb=" C PRO E 74 " pdb=" CB PRO E 74 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA ARG E 306 " pdb=" N ARG E 306 " pdb=" C ARG E 306 " pdb=" CB ARG E 306 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CB ILE E 280 " pdb=" CA ILE E 280 " pdb=" CG1 ILE E 280 " pdb=" CG2 ILE E 280 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 1544 not shown) Planarity restraints: 1664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 73 " 0.075 5.00e-02 4.00e+02 1.11e-01 1.98e+01 pdb=" N PRO E 74 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO E 74 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO E 74 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 95 " -0.039 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO E 96 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO E 96 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 96 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 391 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.90e+00 pdb=" N PRO C 392 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 392 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 392 " 0.028 5.00e-02 4.00e+02 ... (remaining 1661 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 74 2.59 - 3.16: 7945 3.16 - 3.74: 14415 3.74 - 4.32: 18971 4.32 - 4.90: 30974 Nonbonded interactions: 72379 Sorted by model distance: nonbonded pdb="MG MG F 301 " pdb=" O3G ANP F 302 " model vdw 2.007 2.170 nonbonded pdb="MG MG D 301 " pdb=" O3G ANP D 302 " model vdw 2.021 2.170 nonbonded pdb="MG MG D 301 " pdb=" O2B ANP D 302 " model vdw 2.059 2.170 nonbonded pdb="MG MG F 301 " pdb=" O2B ANP F 302 " model vdw 2.079 2.170 nonbonded pdb=" O1B ANP F 302 " pdb=" O3G ANP F 302 " model vdw 2.081 3.040 ... (remaining 72374 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 'D' selection = (chain 'F' and (resid 2 through 22 or (resid 23 and (name N or name CA or name C \ or name O or name CB )) or resid 24 through 302)) } 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 group one per residue 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: 1.180 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.860 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 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 : 0.005 0.146 9542 Z= 0.250 Angle : 0.869 17.473 12982 Z= 0.458 Chirality : 0.050 0.327 1547 Planarity : 0.005 0.111 1664 Dihedral : 15.814 176.965 3464 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.91 % Favored : 95.77 % Rotamer: Outliers : 1.36 % Allowed : 0.42 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.24), residues: 1253 helix: 0.29 (0.22), residues: 589 sheet: -0.19 (0.42), residues: 160 loop : -1.51 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 138 TYR 0.009 0.001 TYR C 128 PHE 0.014 0.001 PHE E 13 TRP 0.015 0.001 TRP C 246 HIS 0.002 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 9542) covalent geometry : angle 0.86866 (12982) hydrogen bonds : bond 0.12782 ( 503) hydrogen bonds : angle 6.17404 ( 1458) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 197 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 344 MET cc_start: 0.1542 (tpp) cc_final: 0.1118 (tpt) REVERT: E 68 ILE cc_start: 0.6692 (OUTLIER) cc_final: 0.6435 (tp) REVERT: E 69 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.6025 (mt-10) REVERT: E 72 ASP cc_start: 0.4498 (OUTLIER) cc_final: 0.4091 (m-30) REVERT: F 46 SER cc_start: 0.7564 (OUTLIER) cc_final: 0.7071 (t) REVERT: F 147 SER cc_start: 0.8906 (p) cc_final: 0.8300 (p) REVERT: F 182 ASP cc_start: 0.6877 (m-30) cc_final: 0.6601 (m-30) REVERT: F 210 LYS cc_start: 0.7896 (tttp) cc_final: 0.7602 (tppt) outliers start: 13 outliers final: 0 residues processed: 206 average time/residue: 0.0848 time to fit residues: 24.6779 Evaluate side-chains 159 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 155 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain F residue 46 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.0010 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN C 181 GLN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN E 122 GLN E 201 HIS E 286 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.208754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.164723 restraints weight = 13238.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.162531 restraints weight = 9616.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.164406 restraints weight = 7368.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.165092 restraints weight = 5873.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.165359 restraints weight = 5238.647| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 9542 Z= 0.131 Angle : 0.641 7.617 12982 Z= 0.314 Chirality : 0.045 0.253 1547 Planarity : 0.005 0.116 1664 Dihedral : 11.656 173.196 1408 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.01 % Rotamer: Outliers : 1.78 % Allowed : 11.09 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.24), residues: 1253 helix: 0.46 (0.22), residues: 597 sheet: -0.19 (0.40), residues: 170 loop : -1.56 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 17 TYR 0.009 0.001 TYR E 260 PHE 0.021 0.001 PHE C 51 TRP 0.013 0.001 TRP C 246 HIS 0.002 0.000 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9542) covalent geometry : angle 0.64058 (12982) hydrogen bonds : bond 0.03808 ( 503) hydrogen bonds : angle 5.10623 ( 1458) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 201 MET cc_start: 0.6949 (tpp) cc_final: 0.6724 (tpp) REVERT: C 262 MET cc_start: 0.7868 (ptm) cc_final: 0.7569 (ptp) REVERT: D 110 MET cc_start: 0.8099 (tpp) cc_final: 0.7539 (tpp) REVERT: E 68 ILE cc_start: 0.7078 (OUTLIER) cc_final: 0.6224 (tp) REVERT: E 69 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: F 182 ASP cc_start: 0.6986 (m-30) cc_final: 0.6620 (m-30) REVERT: F 212 MET cc_start: 0.6583 (ttm) cc_final: 0.6380 (ttm) outliers start: 17 outliers final: 7 residues processed: 176 average time/residue: 0.0813 time to fit residues: 20.4786 Evaluate side-chains 157 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 284 CYS Chi-restraints excluded: chain F residue 89 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 58 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 97 optimal weight: 0.0170 chunk 23 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 61 optimal weight: 0.1980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN C 294 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 GLN D 163 ASN E 122 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.209089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.163754 restraints weight = 13313.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.163681 restraints weight = 9670.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.166294 restraints weight = 7353.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.166177 restraints weight = 5404.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.166301 restraints weight = 5603.874| |-----------------------------------------------------------------------------| r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 9542 Z= 0.116 Angle : 0.601 11.124 12982 Z= 0.293 Chirality : 0.043 0.219 1547 Planarity : 0.005 0.107 1664 Dihedral : 11.036 172.710 1405 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.75 % Favored : 96.17 % Rotamer: Outliers : 2.41 % Allowed : 14.02 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.24), residues: 1253 helix: 0.61 (0.22), residues: 603 sheet: -0.12 (0.41), residues: 160 loop : -1.56 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 261 TYR 0.012 0.001 TYR C 199 PHE 0.008 0.001 PHE F 185 TRP 0.012 0.001 TRP E 75 HIS 0.004 0.000 HIS E 376 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9542) covalent geometry : angle 0.60116 (12982) hydrogen bonds : bond 0.03527 ( 503) hydrogen bonds : angle 4.84732 ( 1458) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 262 MET cc_start: 0.7937 (ptm) cc_final: 0.7644 (ptp) REVERT: D 106 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: E 68 ILE cc_start: 0.6917 (OUTLIER) cc_final: 0.6109 (tp) REVERT: E 69 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7261 (mp0) REVERT: F 27 ASN cc_start: 0.7112 (t0) cc_final: 0.6885 (t0) REVERT: F 38 MET cc_start: 0.6524 (tpt) cc_final: 0.5889 (mmt) REVERT: F 182 ASP cc_start: 0.6980 (m-30) cc_final: 0.6714 (m-30) outliers start: 23 outliers final: 14 residues processed: 182 average time/residue: 0.0832 time to fit residues: 21.1510 Evaluate side-chains 163 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 115 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 218 ASN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.205321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.160259 restraints weight = 13407.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.158935 restraints weight = 9184.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.160132 restraints weight = 6999.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.161704 restraints weight = 5679.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.161705 restraints weight = 5002.463| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 9542 Z= 0.145 Angle : 0.631 13.768 12982 Z= 0.303 Chirality : 0.044 0.226 1547 Planarity : 0.005 0.107 1664 Dihedral : 10.629 175.342 1402 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.99 % Favored : 95.93 % Rotamer: Outliers : 3.03 % Allowed : 16.63 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.24), residues: 1253 helix: 0.57 (0.22), residues: 601 sheet: -0.09 (0.40), residues: 160 loop : -1.46 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 261 TYR 0.012 0.001 TYR E 258 PHE 0.014 0.001 PHE E 319 TRP 0.010 0.001 TRP C 246 HIS 0.003 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9542) covalent geometry : angle 0.63123 (12982) hydrogen bonds : bond 0.03564 ( 503) hydrogen bonds : angle 4.78295 ( 1458) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: C 262 MET cc_start: 0.7895 (ptm) cc_final: 0.6650 (ptt) REVERT: C 266 MET cc_start: 0.7513 (mtm) cc_final: 0.7245 (mtm) REVERT: D 54 LEU cc_start: 0.8611 (tp) cc_final: 0.8155 (tp) REVERT: D 106 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: E 68 ILE cc_start: 0.6791 (OUTLIER) cc_final: 0.5885 (tp) REVERT: E 69 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7223 (mp0) REVERT: F 27 ASN cc_start: 0.7108 (t0) cc_final: 0.6839 (t0) REVERT: F 182 ASP cc_start: 0.6864 (m-30) cc_final: 0.6560 (m-30) outliers start: 29 outliers final: 19 residues processed: 180 average time/residue: 0.0855 time to fit residues: 21.4214 Evaluate side-chains 170 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 284 CYS Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 78 optimal weight: 30.0000 chunk 3 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 0.0570 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 76 optimal weight: 30.0000 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.204991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.161513 restraints weight = 13312.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.161397 restraints weight = 11410.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.163314 restraints weight = 8167.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.163115 restraints weight = 6415.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.163404 restraints weight = 5961.155| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 9542 Z= 0.145 Angle : 0.627 10.948 12982 Z= 0.303 Chirality : 0.044 0.211 1547 Planarity : 0.005 0.104 1664 Dihedral : 10.374 175.157 1402 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.07 % Favored : 95.85 % Rotamer: Outliers : 3.45 % Allowed : 17.15 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.24), residues: 1253 helix: 0.66 (0.22), residues: 588 sheet: -0.02 (0.40), residues: 166 loop : -1.48 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 261 TYR 0.015 0.001 TYR C 199 PHE 0.013 0.001 PHE C 51 TRP 0.008 0.001 TRP C 246 HIS 0.002 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9542) covalent geometry : angle 0.62714 (12982) hydrogen bonds : bond 0.03521 ( 503) hydrogen bonds : angle 4.74832 ( 1458) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: C 25 PHE cc_start: 0.6176 (OUTLIER) cc_final: 0.5411 (m-80) REVERT: C 201 MET cc_start: 0.6850 (tpp) cc_final: 0.6596 (tpp) REVERT: C 262 MET cc_start: 0.7793 (ptm) cc_final: 0.6584 (ptt) REVERT: D 106 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: D 110 MET cc_start: 0.8130 (tpp) cc_final: 0.7822 (mmm) REVERT: F 182 ASP cc_start: 0.6641 (m-30) cc_final: 0.6435 (m-30) outliers start: 33 outliers final: 24 residues processed: 174 average time/residue: 0.0890 time to fit residues: 21.4046 Evaluate side-chains 170 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 284 CYS Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 73 optimal weight: 0.2980 chunk 68 optimal weight: 5.9990 chunk 52 optimal weight: 0.0370 chunk 69 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 77 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.207052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.161861 restraints weight = 13222.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.161198 restraints weight = 9023.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.163980 restraints weight = 7009.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.164477 restraints weight = 4891.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.164551 restraints weight = 4880.351| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 9542 Z= 0.117 Angle : 0.599 8.583 12982 Z= 0.291 Chirality : 0.043 0.191 1547 Planarity : 0.004 0.101 1664 Dihedral : 10.144 176.568 1402 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.01 % Rotamer: Outliers : 2.41 % Allowed : 18.62 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.24), residues: 1253 helix: 0.80 (0.22), residues: 586 sheet: -0.12 (0.41), residues: 160 loop : -1.43 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 261 TYR 0.013 0.001 TYR E 258 PHE 0.014 0.001 PHE C 51 TRP 0.008 0.001 TRP C 246 HIS 0.002 0.000 HIS D 53 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9542) covalent geometry : angle 0.59877 (12982) hydrogen bonds : bond 0.03380 ( 503) hydrogen bonds : angle 4.66365 ( 1458) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 25 PHE cc_start: 0.5990 (OUTLIER) cc_final: 0.5183 (m-80) REVERT: C 201 MET cc_start: 0.6773 (tpp) cc_final: 0.6486 (tpp) REVERT: C 262 MET cc_start: 0.7902 (ptm) cc_final: 0.7674 (ptt) REVERT: D 54 LEU cc_start: 0.8505 (tp) cc_final: 0.8240 (tp) REVERT: D 106 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: D 110 MET cc_start: 0.8015 (tpp) cc_final: 0.7771 (mmm) REVERT: E 55 LEU cc_start: 0.8525 (tt) cc_final: 0.8293 (tt) REVERT: E 390 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6012 (tp) outliers start: 23 outliers final: 16 residues processed: 171 average time/residue: 0.1032 time to fit residues: 24.3962 Evaluate side-chains 169 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 117 optimal weight: 0.9980 chunk 8 optimal weight: 0.0670 chunk 122 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 79 optimal weight: 40.0000 chunk 43 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 36 optimal weight: 0.0770 chunk 107 optimal weight: 4.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.207878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.162837 restraints weight = 13482.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.162443 restraints weight = 9245.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.165063 restraints weight = 7389.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.165342 restraints weight = 5005.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.165640 restraints weight = 4975.379| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 9542 Z= 0.115 Angle : 0.605 8.653 12982 Z= 0.293 Chirality : 0.043 0.190 1547 Planarity : 0.004 0.098 1664 Dihedral : 10.039 177.752 1402 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.99 % Favored : 95.93 % Rotamer: Outliers : 2.62 % Allowed : 19.56 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.24), residues: 1253 helix: 0.90 (0.22), residues: 586 sheet: -0.08 (0.41), residues: 160 loop : -1.41 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 261 TYR 0.017 0.001 TYR C 199 PHE 0.009 0.001 PHE E 319 TRP 0.008 0.001 TRP C 246 HIS 0.002 0.000 HIS D 53 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9542) covalent geometry : angle 0.60548 (12982) hydrogen bonds : bond 0.03313 ( 503) hydrogen bonds : angle 4.60315 ( 1458) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 25 PHE cc_start: 0.5893 (OUTLIER) cc_final: 0.5131 (m-80) REVERT: C 262 MET cc_start: 0.7856 (ptm) cc_final: 0.7580 (ptt) REVERT: D 106 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: D 110 MET cc_start: 0.8078 (tpp) cc_final: 0.7865 (mmm) REVERT: E 55 LEU cc_start: 0.8463 (tt) cc_final: 0.8193 (tt) outliers start: 25 outliers final: 14 residues processed: 171 average time/residue: 0.0980 time to fit residues: 23.2870 Evaluate side-chains 167 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 66 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 7 optimal weight: 7.9990 chunk 115 optimal weight: 0.0980 chunk 96 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 120 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.205698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.160575 restraints weight = 13452.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.160540 restraints weight = 9024.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.162876 restraints weight = 7178.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.162857 restraints weight = 5325.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.163318 restraints weight = 5030.293| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 9542 Z= 0.133 Angle : 0.622 8.915 12982 Z= 0.301 Chirality : 0.043 0.205 1547 Planarity : 0.004 0.096 1664 Dihedral : 10.065 179.478 1402 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.15 % Favored : 95.77 % Rotamer: Outliers : 2.51 % Allowed : 20.50 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.24), residues: 1253 helix: 0.81 (0.22), residues: 587 sheet: -0.16 (0.41), residues: 160 loop : -1.39 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 261 TYR 0.013 0.001 TYR F 15 PHE 0.023 0.001 PHE F 68 TRP 0.009 0.001 TRP E 75 HIS 0.002 0.000 HIS E 376 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 9542) covalent geometry : angle 0.62163 (12982) hydrogen bonds : bond 0.03374 ( 503) hydrogen bonds : angle 4.62467 ( 1458) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: C 25 PHE cc_start: 0.5938 (OUTLIER) cc_final: 0.5145 (m-80) REVERT: C 195 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7578 (mt-10) REVERT: C 262 MET cc_start: 0.7859 (ptm) cc_final: 0.7356 (ptt) REVERT: D 106 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: D 110 MET cc_start: 0.8119 (tpp) cc_final: 0.7871 (mmm) REVERT: D 212 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7060 (mpt) REVERT: E 55 LEU cc_start: 0.8511 (tt) cc_final: 0.8182 (tt) outliers start: 24 outliers final: 16 residues processed: 176 average time/residue: 0.1025 time to fit residues: 25.0908 Evaluate side-chains 173 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 284 CYS Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 150 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 5 optimal weight: 3.9990 chunk 121 optimal weight: 0.3980 chunk 86 optimal weight: 0.0570 chunk 10 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 25 optimal weight: 0.0370 chunk 65 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.207757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.163438 restraints weight = 13359.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.162563 restraints weight = 9008.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.165840 restraints weight = 7249.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.165858 restraints weight = 5085.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.166055 restraints weight = 4890.056| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 9542 Z= 0.112 Angle : 0.613 11.243 12982 Z= 0.295 Chirality : 0.043 0.188 1547 Planarity : 0.004 0.093 1664 Dihedral : 9.949 177.058 1402 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.67 % Favored : 96.25 % Rotamer: Outliers : 2.51 % Allowed : 20.92 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.24), residues: 1253 helix: 0.99 (0.22), residues: 582 sheet: -0.12 (0.42), residues: 160 loop : -1.34 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 261 TYR 0.017 0.001 TYR C 199 PHE 0.009 0.001 PHE E 319 TRP 0.008 0.001 TRP C 246 HIS 0.001 0.000 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9542) covalent geometry : angle 0.61326 (12982) hydrogen bonds : bond 0.03252 ( 503) hydrogen bonds : angle 4.56632 ( 1458) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: C 25 PHE cc_start: 0.5856 (OUTLIER) cc_final: 0.4997 (m-80) REVERT: C 195 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7665 (mt-10) REVERT: C 199 TYR cc_start: 0.6587 (p90) cc_final: 0.6336 (p90) REVERT: D 106 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: D 110 MET cc_start: 0.8080 (tpp) cc_final: 0.7814 (mmm) REVERT: D 212 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7105 (mpt) REVERT: E 55 LEU cc_start: 0.8426 (tt) cc_final: 0.8083 (tt) REVERT: E 276 MET cc_start: 0.4445 (mmp) cc_final: 0.3718 (ptt) outliers start: 24 outliers final: 19 residues processed: 176 average time/residue: 0.1023 time to fit residues: 25.1175 Evaluate side-chains 173 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 150 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 45 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 6 optimal weight: 0.4980 chunk 97 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.202184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.156454 restraints weight = 13374.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.155513 restraints weight = 9306.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.158745 restraints weight = 7146.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.158451 restraints weight = 5039.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.158681 restraints weight = 4977.886| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 9542 Z= 0.183 Angle : 0.687 11.082 12982 Z= 0.332 Chirality : 0.045 0.241 1547 Planarity : 0.005 0.091 1664 Dihedral : 10.104 179.937 1402 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.71 % Favored : 95.21 % Rotamer: Outliers : 2.51 % Allowed : 22.38 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.24), residues: 1253 helix: 0.63 (0.22), residues: 584 sheet: -0.22 (0.42), residues: 160 loop : -1.35 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 261 TYR 0.016 0.002 TYR F 15 PHE 0.013 0.001 PHE E 319 TRP 0.012 0.001 TRP E 75 HIS 0.004 0.001 HIS D 141 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 9542) covalent geometry : angle 0.68723 (12982) hydrogen bonds : bond 0.03671 ( 503) hydrogen bonds : angle 4.79172 ( 1458) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: C 25 PHE cc_start: 0.6056 (OUTLIER) cc_final: 0.5195 (m-80) REVERT: D 106 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: D 110 MET cc_start: 0.8241 (tpp) cc_final: 0.7922 (mmm) REVERT: D 212 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7258 (mpt) REVERT: E 55 LEU cc_start: 0.8577 (tt) cc_final: 0.8230 (tt) REVERT: E 201 HIS cc_start: 0.4795 (OUTLIER) cc_final: 0.2939 (p90) outliers start: 24 outliers final: 18 residues processed: 164 average time/residue: 0.1023 time to fit residues: 23.5629 Evaluate side-chains 166 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 150 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 21 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 102 optimal weight: 0.3980 chunk 45 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.204836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.159604 restraints weight = 13227.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.158697 restraints weight = 8948.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.161294 restraints weight = 7147.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.161904 restraints weight = 5102.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.161930 restraints weight = 5117.915| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 9542 Z= 0.128 Angle : 0.644 10.018 12982 Z= 0.310 Chirality : 0.043 0.211 1547 Planarity : 0.004 0.089 1664 Dihedral : 10.074 179.769 1402 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.07 % Favored : 95.85 % Rotamer: Outliers : 2.41 % Allowed : 22.59 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.24), residues: 1253 helix: 0.75 (0.22), residues: 587 sheet: -0.14 (0.42), residues: 160 loop : -1.35 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 261 TYR 0.015 0.001 TYR C 199 PHE 0.011 0.001 PHE E 203 TRP 0.009 0.001 TRP C 246 HIS 0.009 0.001 HIS E 201 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9542) covalent geometry : angle 0.64446 (12982) hydrogen bonds : bond 0.03447 ( 503) hydrogen bonds : angle 4.69330 ( 1458) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1638.32 seconds wall clock time: 28 minutes 55.04 seconds (1735.04 seconds total)