Starting phenix.real_space_refine on Thu Jul 2 23:50:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ao8_11837/07_2026/7ao8_11837_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ao8_11837/07_2026/7ao8_11837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ao8_11837/07_2026/7ao8_11837_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ao8_11837/07_2026/7ao8_11837_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ao8_11837/07_2026/7ao8_11837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ao8_11837/07_2026/7ao8_11837.map" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians K 4 8.98 5 Zn 2 6.06 5 P 12 5.49 5 S 59 5.16 5 C 6897 2.51 5 N 1837 2.21 5 O 2094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10905 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 487 Classifications: {'peptide': 64} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 58} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2206 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 266} Chain breaks: 4 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2206 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 266} Chain breaks: 4 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 2964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2964 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 353} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2964 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 353} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' K': 2} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' K': 2} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C1 IHP D 801 " occ=0.70 ... (34 atoms not shown) pdb=" P6 IHP D 801 " occ=0.70 residue: pdb=" C1 IHP A 801 " occ=0.70 ... (34 atoms not shown) pdb=" P6 IHP A 801 " occ=0.70 Time building chain proxies: 2.17, per 1000 atoms: 0.20 Number of scatterers: 10905 At special positions: 0 Unit cell: (206.01, 85.02, 92.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 K 4 19.00 S 59 16.00 P 12 15.00 O 2094 8.00 N 1837 7.00 C 6897 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: 0.99 Conformation dependent library (CDL) restraints added in 316.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 178 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" ND1 HIS E 178 " 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2522 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 5 sheets defined 43.5% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'C' and resid 189 through 198 Processing helix chain 'C' and resid 199 through 201 No H-bonds generated for 'chain 'C' and resid 199 through 201' Processing helix chain 'D' and resid 131 through 137 Processing helix chain 'D' and resid 190 through 193 Processing helix chain 'D' and resid 206 through 227 Processing helix chain 'D' and resid 238 through 246 Processing helix chain 'D' and resid 247 through 261 Processing helix chain 'D' and resid 264 through 273 removed outlier: 3.791A pdb=" N SER D 270 " --> pdb=" O SER D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 288 Processing helix chain 'D' and resid 289 through 304 removed outlier: 3.620A pdb=" N GLU D 301 " --> pdb=" O GLU D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 314 Processing helix chain 'D' and resid 319 through 331 Processing helix chain 'A' and resid 131 through 137 Processing helix chain 'A' and resid 190 through 193 Processing helix chain 'A' and resid 206 through 227 Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 247 through 261 Processing helix chain 'A' and resid 264 through 273 removed outlier: 3.792A pdb=" N SER A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 289 through 304 removed outlier: 3.620A pdb=" N GLU A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 314 Processing helix chain 'A' and resid 319 through 331 Processing helix chain 'E' and resid 16 through 21 removed outlier: 3.847A pdb=" N GLY E 20 " --> pdb=" O GLY E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 45 removed outlier: 4.142A pdb=" N ARG E 36 " --> pdb=" O PRO E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 51 Processing helix chain 'E' and resid 60 through 65 Processing helix chain 'E' and resid 69 through 79 Processing helix chain 'E' and resid 83 through 94 removed outlier: 3.595A pdb=" N SER E 88 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LYS E 89 " --> pdb=" O SER E 85 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN E 90 " --> pdb=" O GLU E 86 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG E 93 " --> pdb=" O LYS E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 126 Processing helix chain 'E' and resid 154 through 164 Processing helix chain 'E' and resid 180 through 187 removed outlier: 3.556A pdb=" N PHE E 187 " --> pdb=" O VAL E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 220 Processing helix chain 'E' and resid 233 through 253 Proline residue: E 243 - end of helix Processing helix chain 'E' and resid 277 through 291 removed outlier: 3.646A pdb=" N CYS E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL E 285 " --> pdb=" O HIS E 281 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE E 291 " --> pdb=" O PHE E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 320 Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 355 through 372 removed outlier: 3.527A pdb=" N ILE E 362 " --> pdb=" O TYR E 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 21 removed outlier: 3.848A pdb=" N GLY B 20 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 45 removed outlier: 4.143A pdb=" N ARG B 36 " --> pdb=" O PRO B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 60 through 65 Processing helix chain 'B' and resid 69 through 79 Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.594A pdb=" N SER B 88 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LYS B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLN B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 93 " --> pdb=" O LYS B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 126 Processing helix chain 'B' and resid 154 through 164 Processing helix chain 'B' and resid 180 through 187 removed outlier: 3.556A pdb=" N PHE B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 220 Processing helix chain 'B' and resid 233 through 253 Proline residue: B 243 - end of helix Processing helix chain 'B' and resid 277 through 291 removed outlier: 3.646A pdb=" N CYS B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL B 285 " --> pdb=" O HIS B 281 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 320 Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 355 through 372 removed outlier: 3.527A pdb=" N ILE B 362 " --> pdb=" O TYR B 358 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 150 through 151 Processing sheet with id=AA2, first strand: chain 'D' and resid 146 through 149 removed outlier: 4.238A pdb=" N TYR D 11 " --> pdb=" O CYS D 126 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU D 23 " --> pdb=" O PHE D 14 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ARG D 25 " --> pdb=" O PHE D 45 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE D 45 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ILE D 27 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL D 43 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLN D 113 " --> pdb=" O CYS D 44 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N TYR D 46 " --> pdb=" O SER D 111 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N SER D 111 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LEU D 110 " --> pdb=" O TYR D 153 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 195 through 199 removed outlier: 6.268A pdb=" N ILE E 53 " --> pdb=" O VAL D 198 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL E 11 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N TYR E 54 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N TYR E 13 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N CYS E 12 " --> pdb=" O VAL E 133 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL E 257 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LEU E 298 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU E 259 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU E 171 " --> pdb=" O VAL E 258 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N GLN E 260 " --> pdb=" O LEU E 171 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE E 173 " --> pdb=" O GLN E 260 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL E 224 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N THR E 195 " --> pdb=" O VAL E 224 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N TYR E 226 " --> pdb=" O THR E 195 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N SER E 197 " --> pdb=" O TYR E 226 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU E 228 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N HIS E 199 " --> pdb=" O LEU E 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 149 removed outlier: 4.237A pdb=" N TYR A 11 " --> pdb=" O CYS A 126 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 23 " --> pdb=" O PHE A 14 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ARG A 25 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE A 45 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ILE A 27 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A 43 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLN A 113 " --> pdb=" O CYS A 44 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N TYR A 46 " --> pdb=" O SER A 111 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER A 111 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU A 110 " --> pdb=" O TYR A 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 195 through 199 removed outlier: 6.270A pdb=" N ILE B 53 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL B 11 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N TYR B 54 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N TYR B 13 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS B 12 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL B 257 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LEU B 298 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU B 259 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU B 171 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLN B 260 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE B 173 " --> pdb=" O GLN B 260 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL B 224 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N THR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N TYR B 226 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER B 197 " --> pdb=" O TYR B 226 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU B 228 " --> pdb=" O SER B 197 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N HIS B 199 " --> pdb=" O LEU B 228 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1218 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: 1.23 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1815 1.31 - 1.44: 3183 1.44 - 1.57: 6036 1.57 - 1.70: 23 1.70 - 1.83: 95 Bond restraints: 11152 Sorted by residual: bond pdb=" CA ILE A 51 " pdb=" C ILE A 51 " ideal model delta sigma weight residual 1.523 1.457 0.066 1.27e-02 6.20e+03 2.74e+01 bond pdb=" CA ILE D 51 " pdb=" C ILE D 51 " ideal model delta sigma weight residual 1.523 1.457 0.066 1.27e-02 6.20e+03 2.71e+01 bond pdb=" CA ILE D 51 " pdb=" CB ILE D 51 " ideal model delta sigma weight residual 1.540 1.472 0.068 1.36e-02 5.41e+03 2.47e+01 bond pdb=" CA ILE A 51 " pdb=" CB ILE A 51 " ideal model delta sigma weight residual 1.540 1.473 0.067 1.36e-02 5.41e+03 2.44e+01 bond pdb=" C GLY E 299 " pdb=" O GLY E 299 " ideal model delta sigma weight residual 1.235 1.178 0.057 1.35e-02 5.49e+03 1.79e+01 ... (remaining 11147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 13033 2.08 - 4.16: 1712 4.16 - 6.24: 289 6.24 - 8.32: 45 8.32 - 10.40: 17 Bond angle restraints: 15096 Sorted by residual: angle pdb=" CA ASN A 31 " pdb=" CB ASN A 31 " pdb=" CG ASN A 31 " ideal model delta sigma weight residual 112.60 105.88 6.72 1.00e+00 1.00e+00 4.52e+01 angle pdb=" CA ASN D 31 " pdb=" CB ASN D 31 " pdb=" CG ASN D 31 " ideal model delta sigma weight residual 112.60 105.91 6.69 1.00e+00 1.00e+00 4.47e+01 angle pdb=" C ARG D 143 " pdb=" N GLU D 144 " pdb=" CA GLU D 144 " ideal model delta sigma weight residual 120.28 129.61 -9.33 1.44e+00 4.82e-01 4.20e+01 angle pdb=" C ARG A 143 " pdb=" N GLU A 144 " pdb=" CA GLU A 144 " ideal model delta sigma weight residual 120.28 129.46 -9.18 1.44e+00 4.82e-01 4.07e+01 angle pdb=" C GLY D 36 " pdb=" N ASN D 37 " pdb=" CA ASN D 37 " ideal model delta sigma weight residual 120.71 129.68 -8.97 1.42e+00 4.96e-01 3.99e+01 ... (remaining 15091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.14: 6195 24.14 - 48.28: 372 48.28 - 72.42: 59 72.42 - 96.56: 26 96.56 - 120.70: 12 Dihedral angle restraints: 6664 sinusoidal: 2718 harmonic: 3946 Sorted by residual: dihedral pdb=" C SER D 52 " pdb=" N SER D 52 " pdb=" CA SER D 52 " pdb=" CB SER D 52 " ideal model delta harmonic sigma weight residual -122.60 -138.48 15.88 0 2.50e+00 1.60e-01 4.04e+01 dihedral pdb=" C SER A 52 " pdb=" N SER A 52 " pdb=" CA SER A 52 " pdb=" CB SER A 52 " ideal model delta harmonic sigma weight residual -122.60 -138.42 15.82 0 2.50e+00 1.60e-01 4.01e+01 dihedral pdb=" C HIS A 101 " pdb=" N HIS A 101 " pdb=" CA HIS A 101 " pdb=" CB HIS A 101 " ideal model delta harmonic sigma weight residual -122.60 -135.95 13.35 0 2.50e+00 1.60e-01 2.85e+01 ... (remaining 6661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.007: 1592 1.007 - 2.013: 0 2.013 - 3.020: 0 3.020 - 4.027: 0 4.027 - 5.034: 4 Chirality restraints: 1596 Sorted by residual: chirality pdb=" C2 IHP D 801 " pdb=" C1 IHP D 801 " pdb=" C3 IHP D 801 " pdb=" O12 IHP D 801 " both_signs ideal model delta sigma weight residual False -2.52 2.51 -5.03 2.00e-01 2.50e+01 6.33e+02 chirality pdb=" C2 IHP A 801 " pdb=" C1 IHP A 801 " pdb=" C3 IHP A 801 " pdb=" O12 IHP A 801 " both_signs ideal model delta sigma weight residual False -2.52 2.51 -5.03 2.00e-01 2.50e+01 6.33e+02 chirality pdb=" C3 IHP D 801 " pdb=" C2 IHP D 801 " pdb=" C4 IHP D 801 " pdb=" O13 IHP D 801 " both_signs ideal model delta sigma weight residual False -2.34 2.39 -4.73 2.00e-01 2.50e+01 5.60e+02 ... (remaining 1593 not shown) Planarity restraints: 1946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 109 " 0.271 2.00e-02 2.50e+03 1.86e-01 6.05e+02 pdb=" CG PHE D 109 " -0.115 2.00e-02 2.50e+03 pdb=" CD1 PHE D 109 " -0.147 2.00e-02 2.50e+03 pdb=" CD2 PHE D 109 " -0.260 2.00e-02 2.50e+03 pdb=" CE1 PHE D 109 " -0.043 2.00e-02 2.50e+03 pdb=" CE2 PHE D 109 " 0.045 2.00e-02 2.50e+03 pdb=" CZ PHE D 109 " 0.249 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 109 " -0.271 2.00e-02 2.50e+03 1.86e-01 6.04e+02 pdb=" CG PHE A 109 " 0.116 2.00e-02 2.50e+03 pdb=" CD1 PHE A 109 " 0.147 2.00e-02 2.50e+03 pdb=" CD2 PHE A 109 " 0.260 2.00e-02 2.50e+03 pdb=" CE1 PHE A 109 " 0.043 2.00e-02 2.50e+03 pdb=" CE2 PHE A 109 " -0.047 2.00e-02 2.50e+03 pdb=" CZ PHE A 109 " -0.247 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 153 " -0.085 2.00e-02 2.50e+03 5.85e-02 6.85e+01 pdb=" CG TYR A 153 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR A 153 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR A 153 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR A 153 " 0.059 2.00e-02 2.50e+03 pdb=" CE2 TYR A 153 " 0.047 2.00e-02 2.50e+03 pdb=" CZ TYR A 153 " 0.025 2.00e-02 2.50e+03 pdb=" OH TYR A 153 " -0.110 2.00e-02 2.50e+03 ... (remaining 1943 not shown) Histogram of nonbonded interaction distances: 1.22 - 2.00: 13 2.00 - 2.79: 2213 2.79 - 3.57: 17734 3.57 - 4.36: 34180 4.36 - 5.14: 56741 Nonbonded interactions: 110881 Sorted by model distance: nonbonded pdb=" OD1 ASP D 163 " pdb=" OE1 GLN E 353 " model vdw 1.219 3.040 nonbonded pdb=" CB PRO C 153 " pdb=" SD MET B 84 " model vdw 1.235 3.800 nonbonded pdb=" CG ASP D 163 " pdb=" OE1 GLN E 353 " model vdw 1.299 3.270 nonbonded pdb=" OE1 GLU D 135 " pdb=" NZ LYS E 361 " model vdw 1.611 3.120 nonbonded pdb=" CG1 ILE C 165 " pdb=" O GLU A 301 " model vdw 1.766 3.440 ... (remaining 110876 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } 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=0.70 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: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.120 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3126 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 : 0.011 0.191 11154 Z= 0.720 Angle : 1.515 10.400 15096 Z= 0.983 Chirality : 0.259 5.034 1596 Planarity : 0.011 0.186 1946 Dihedral : 17.193 120.702 4142 Min Nonbonded Distance : 1.219 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.87 % Favored : 92.52 % Rotamer: Outliers : 4.18 % Allowed : 7.06 % Favored : 88.76 % Cbeta Deviations : 0.63 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.19), residues: 1324 helix: -2.91 (0.16), residues: 544 sheet: -1.04 (0.36), residues: 180 loop : -1.95 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.003 ARG A 25 TYR 0.110 0.008 TYR D 153 PHE 0.271 0.012 PHE A 109 TRP 0.023 0.004 TRP C 159 HIS 0.009 0.002 HIS D 121 Details of bonding type rmsd/Z covalent geometry : bond 0.01094 / 0.71 (11152) covalent geometry : angle 1.51470 / 0.98 (15096) hydrogen bonds : bond 0.22740 / 14.80 ( 426) hydrogen bonds : angle 8.80789 / 6.07 ( 1218) metal coordination : bond 0.19074 / 9.57 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 144 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 42 VAL cc_start: 0.3628 (OUTLIER) cc_final: 0.3321 (m) REVERT: A 269 ILE cc_start: 0.6793 (OUTLIER) cc_final: 0.6423 (tp) REVERT: E 47 LEU cc_start: 0.8178 (mt) cc_final: 0.7760 (mm) REVERT: E 82 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7672 (m-30) REVERT: B 45 TYR cc_start: 0.6913 (m-80) cc_final: 0.6488 (m-80) REVERT: B 82 ASP cc_start: 0.4851 (OUTLIER) cc_final: 0.4416 (m-30) REVERT: B 313 THR cc_start: 0.7810 (m) cc_final: 0.7439 (m) outliers start: 48 outliers final: 2 residues processed: 187 average time/residue: 0.0927 time to fit residues: 24.0236 Evaluate side-chains 88 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 10.0000 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 197 GLN D 261 ASN A 197 GLN A 261 ASN E 26 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 HIS E 128 GLN ** E 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 HIS E 225 ASN E 354 ASN B 26 GLN ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 HIS ** B 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN B 225 ASN B 354 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.081638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.062945 restraints weight = 89307.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.064275 restraints weight = 72251.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.065229 restraints weight = 60825.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.066170 restraints weight = 53379.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.066831 restraints weight = 47617.833| |-----------------------------------------------------------------------------| r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4198 r_free = 0.4198 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4199 r_free = 0.4199 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.4199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5800 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11154 Z= 0.131 Angle : 0.653 10.237 15096 Z= 0.336 Chirality : 0.046 0.398 1596 Planarity : 0.004 0.037 1946 Dihedral : 6.242 50.238 1580 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.17 % Allowed : 2.44 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.22), residues: 1324 helix: 0.13 (0.22), residues: 538 sheet: -0.62 (0.37), residues: 184 loop : -0.95 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 188 TYR 0.021 0.002 TYR E 237 PHE 0.016 0.002 PHE B 150 TRP 0.012 0.001 TRP C 159 HIS 0.006 0.001 HIS E 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (11152) covalent geometry : angle 0.65317 / 0.34 (15096) hydrogen bonds : bond 0.04292 / 2.76 ( 426) hydrogen bonds : angle 5.07180 / 3.50 ( 1218) metal coordination : bond 0.00300 / 0.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 285 MET cc_start: 0.7123 (tmm) cc_final: 0.6588 (tmm) REVERT: E 51 MET cc_start: 0.8017 (pmm) cc_final: 0.7513 (pmm) REVERT: E 245 MET cc_start: 0.8479 (mmp) cc_final: 0.7421 (tpt) REVERT: E 249 MET cc_start: 0.7425 (tpt) cc_final: 0.7029 (tpt) REVERT: E 266 LEU cc_start: 0.8523 (mt) cc_final: 0.8277 (mm) REVERT: E 324 ILE cc_start: 0.7147 (pt) cc_final: 0.6335 (pt) REVERT: B 62 GLU cc_start: 0.9299 (tp30) cc_final: 0.9039 (mp0) REVERT: B 81 PRO cc_start: 0.6068 (Cg_exo) cc_final: 0.5590 (Cg_endo) REVERT: B 84 MET cc_start: 0.5344 (mtp) cc_final: 0.5126 (mmm) REVERT: B 141 HIS cc_start: 0.7657 (m-70) cc_final: 0.7390 (m-70) REVERT: B 152 TYR cc_start: 0.5354 (m-80) cc_final: 0.4988 (m-10) REVERT: B 259 LEU cc_start: 0.7735 (tp) cc_final: 0.7037 (tp) REVERT: B 289 LYS cc_start: 0.8428 (tttm) cc_final: 0.7904 (tptt) REVERT: B 295 MET cc_start: -0.2629 (mtt) cc_final: -0.3988 (tpp) REVERT: B 324 ILE cc_start: 0.7543 (pt) cc_final: 0.6566 (pt) outliers start: 2 outliers final: 1 residues processed: 105 average time/residue: 0.1045 time to fit residues: 16.1966 Evaluate side-chains 81 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 85 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 0 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 chunk 125 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 203 ASN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 ASN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN B 39 HIS ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 GLN B 353 GLN B 369 ASN B 375 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.061630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.044246 restraints weight = 102564.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.045230 restraints weight = 79464.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.045993 restraints weight = 65864.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.046469 restraints weight = 57173.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.046988 restraints weight = 51771.849| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.8028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 11154 Z= 0.322 Angle : 0.970 16.558 15096 Z= 0.506 Chirality : 0.052 0.339 1596 Planarity : 0.007 0.055 1946 Dihedral : 7.607 58.157 1580 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 25.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.09 % Allowed : 5.49 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.21), residues: 1324 helix: -0.92 (0.21), residues: 547 sheet: -0.96 (0.39), residues: 156 loop : -1.29 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 212 TYR 0.044 0.004 TYR B 237 PHE 0.035 0.004 PHE B 198 TRP 0.023 0.004 TRP B 135 HIS 0.013 0.003 HIS E 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00657 / 0.32 (11152) covalent geometry : angle 0.97027 / 0.51 (15096) hydrogen bonds : bond 0.06282 / 4.07 ( 426) hydrogen bonds : angle 6.11920 / 4.15 ( 1218) metal coordination : bond 0.00510 / 0.25 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 285 MET cc_start: 0.4328 (tmm) cc_final: 0.4049 (tmm) REVERT: D 329 MET cc_start: 0.9272 (ttp) cc_final: 0.8785 (ppp) REVERT: A 329 MET cc_start: 0.9250 (mpp) cc_final: 0.8946 (mpp) REVERT: E 51 MET cc_start: 0.8691 (pmm) cc_final: 0.8217 (pmm) REVERT: E 140 HIS cc_start: 0.7272 (p90) cc_final: 0.7007 (p-80) REVERT: B 64 MET cc_start: 0.5675 (mtt) cc_final: 0.5064 (mtt) REVERT: B 241 PHE cc_start: 0.8727 (t80) cc_final: 0.8285 (t80) REVERT: B 259 LEU cc_start: 0.8550 (tp) cc_final: 0.7952 (tp) REVERT: B 289 LYS cc_start: 0.8711 (tttm) cc_final: 0.8362 (tptt) outliers start: 1 outliers final: 1 residues processed: 81 average time/residue: 0.1085 time to fit residues: 12.8256 Evaluate side-chains 63 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 3 optimal weight: 20.0000 chunk 6 optimal weight: 30.0000 chunk 63 optimal weight: 0.9980 chunk 15 optimal weight: 30.0000 chunk 116 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 0.0980 chunk 94 optimal weight: 0.0030 chunk 79 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 overall best weight: 1.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 GLN ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 ASN E 179 HIS B 26 GLN B 39 HIS ** B 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.063450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.045608 restraints weight = 103993.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.046760 restraints weight = 77701.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.047674 restraints weight = 63062.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.048263 restraints weight = 53785.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.048745 restraints weight = 47884.517| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3823 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3823 r_free = 0.3823 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3823 r_free = 0.3823 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.8015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11154 Z= 0.121 Angle : 0.604 8.461 15096 Z= 0.316 Chirality : 0.042 0.280 1596 Planarity : 0.004 0.046 1946 Dihedral : 6.730 58.583 1580 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.22), residues: 1324 helix: 0.23 (0.22), residues: 546 sheet: -0.72 (0.39), residues: 156 loop : -1.13 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 77 TYR 0.018 0.001 TYR E 72 PHE 0.025 0.002 PHE E 241 TRP 0.010 0.001 TRP A 330 HIS 0.007 0.001 HIS E 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (11152) covalent geometry : angle 0.60365 / 0.32 (15096) hydrogen bonds : bond 0.04096 / 2.63 ( 426) hydrogen bonds : angle 5.01646 / 3.44 ( 1218) metal coordination : bond 0.00112 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 285 MET cc_start: 0.6012 (tmm) cc_final: 0.5706 (tmm) REVERT: D 329 MET cc_start: 0.8961 (ttp) cc_final: 0.8205 (ppp) REVERT: E 245 MET cc_start: 0.9254 (mpp) cc_final: 0.8885 (mpp) REVERT: B 64 MET cc_start: 0.5623 (mtt) cc_final: 0.5183 (mtt) REVERT: B 175 ILE cc_start: 0.9324 (pt) cc_final: 0.8954 (mm) REVERT: B 237 TYR cc_start: 0.8823 (t80) cc_final: 0.7999 (t80) REVERT: B 259 LEU cc_start: 0.8938 (tp) cc_final: 0.8375 (tp) REVERT: B 289 LYS cc_start: 0.8726 (tttm) cc_final: 0.8410 (tptt) REVERT: B 311 CYS cc_start: 0.9349 (t) cc_final: 0.9073 (t) REVERT: B 315 GLU cc_start: 0.8769 (pp20) cc_final: 0.8542 (pt0) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.0867 time to fit residues: 11.0469 Evaluate side-chains 67 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 37 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 191 GLN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 ASN B 26 GLN ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN B 253 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.059505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.042396 restraints weight = 106392.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.043502 restraints weight = 79225.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.044229 restraints weight = 63713.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.044845 restraints weight = 54895.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.045380 restraints weight = 48753.576| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3726 r_free = 0.3726 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.9276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11154 Z= 0.186 Angle : 0.660 7.573 15096 Z= 0.350 Chirality : 0.043 0.205 1596 Planarity : 0.005 0.043 1946 Dihedral : 6.870 59.132 1580 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.23), residues: 1324 helix: 0.24 (0.22), residues: 541 sheet: -1.07 (0.39), residues: 158 loop : -1.06 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 172 TYR 0.025 0.002 TYR E 72 PHE 0.021 0.002 PHE E 241 TRP 0.011 0.002 TRP D 199 HIS 0.008 0.002 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.19 (11152) covalent geometry : angle 0.66035 / 0.35 (15096) hydrogen bonds : bond 0.04342 / 2.81 ( 426) hydrogen bonds : angle 5.06460 / 3.48 ( 1218) metal coordination : bond 0.00339 / 0.17 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 329 MET cc_start: 0.9075 (ttp) cc_final: 0.8856 (tpp) REVERT: A 329 MET cc_start: 0.9011 (mpp) cc_final: 0.8742 (mpp) REVERT: E 140 HIS cc_start: 0.6877 (p90) cc_final: 0.6655 (p-80) REVERT: E 241 PHE cc_start: 0.8734 (t80) cc_final: 0.8494 (t80) REVERT: E 245 MET cc_start: 0.9422 (mpp) cc_final: 0.9053 (mpp) REVERT: E 249 MET cc_start: 0.8065 (tpt) cc_final: 0.7857 (tpt) REVERT: B 64 MET cc_start: 0.6454 (mtt) cc_final: 0.5989 (mtt) REVERT: B 237 TYR cc_start: 0.8895 (t80) cc_final: 0.8537 (t80) REVERT: B 278 ILE cc_start: 0.9319 (mt) cc_final: 0.9009 (tt) REVERT: B 289 LYS cc_start: 0.8850 (tttm) cc_final: 0.8508 (tptt) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0822 time to fit residues: 8.9580 Evaluate side-chains 61 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 131 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 34 optimal weight: 30.0000 chunk 108 optimal weight: 0.4980 chunk 96 optimal weight: 0.6980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 174 GLN E 28 HIS E 40 ASN ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.059525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.042277 restraints weight = 107679.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.043419 restraints weight = 79383.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.044284 restraints weight = 63642.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.044871 restraints weight = 54076.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.045350 restraints weight = 48056.056| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3726 r_free = 0.3726 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3726 r_free = 0.3726 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.9819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11154 Z= 0.152 Angle : 0.598 7.775 15096 Z= 0.316 Chirality : 0.042 0.213 1596 Planarity : 0.004 0.043 1946 Dihedral : 6.671 59.489 1580 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.23), residues: 1324 helix: 0.40 (0.22), residues: 550 sheet: -1.10 (0.39), residues: 154 loop : -1.07 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 371 TYR 0.020 0.002 TYR E 336 PHE 0.015 0.002 PHE B 198 TRP 0.009 0.001 TRP D 330 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (11152) covalent geometry : angle 0.59757 / 0.32 (15096) hydrogen bonds : bond 0.03995 / 2.57 ( 426) hydrogen bonds : angle 5.02663 / 3.47 ( 1218) metal coordination : bond 0.00254 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 329 MET cc_start: 0.9072 (ttp) cc_final: 0.8504 (ptp) REVERT: A 329 MET cc_start: 0.8856 (mpp) cc_final: 0.8645 (mpp) REVERT: E 350 MET cc_start: 0.5539 (ppp) cc_final: 0.5226 (ppp) REVERT: B 64 MET cc_start: 0.6802 (mtt) cc_final: 0.6352 (mtt) REVERT: B 237 TYR cc_start: 0.8791 (t80) cc_final: 0.8483 (t80) REVERT: B 263 SER cc_start: 0.8657 (t) cc_final: 0.8420 (p) REVERT: B 278 ILE cc_start: 0.9334 (mt) cc_final: 0.9068 (tt) REVERT: B 289 LYS cc_start: 0.8907 (tttm) cc_final: 0.8634 (tptt) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0948 time to fit residues: 9.6242 Evaluate side-chains 59 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 5 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 88 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 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 = 0.4160 r_free = 0.4160 target = 0.058966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.041867 restraints weight = 107678.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.042956 restraints weight = 78767.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.043785 restraints weight = 63337.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.044305 restraints weight = 53867.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.044748 restraints weight = 48257.559| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (17 function evaluations) r_final: 0.3717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 1.0375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11154 Z= 0.131 Angle : 0.572 7.109 15096 Z= 0.300 Chirality : 0.041 0.190 1596 Planarity : 0.004 0.045 1946 Dihedral : 6.442 55.796 1580 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.23), residues: 1324 helix: 0.59 (0.22), residues: 546 sheet: -0.96 (0.41), residues: 154 loop : -1.13 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 36 TYR 0.014 0.002 TYR E 172 PHE 0.012 0.002 PHE E 341 TRP 0.009 0.001 TRP A 288 HIS 0.006 0.001 HIS E 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (11152) covalent geometry : angle 0.57209 / 0.30 (15096) hydrogen bonds : bond 0.03750 / 2.41 ( 426) hydrogen bonds : angle 4.82146 / 3.32 ( 1218) metal coordination : bond 0.00176 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: D 329 MET cc_start: 0.8909 (ttp) cc_final: 0.8384 (ptp) REVERT: E 295 MET cc_start: 0.5032 (mmt) cc_final: 0.4825 (mmt) REVERT: E 350 MET cc_start: 0.5473 (ppp) cc_final: 0.5195 (ppp) REVERT: B 64 MET cc_start: 0.6927 (mtt) cc_final: 0.6506 (mtt) REVERT: B 237 TYR cc_start: 0.8820 (t80) cc_final: 0.8327 (t80) REVERT: B 278 ILE cc_start: 0.9275 (mt) cc_final: 0.8998 (tt) REVERT: B 289 LYS cc_start: 0.8960 (tttm) cc_final: 0.8700 (tptt) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0800 time to fit residues: 8.2079 Evaluate side-chains 58 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 2 optimal weight: 40.0000 chunk 130 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 4 optimal weight: 30.0000 chunk 126 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 56 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 102 GLN A 102 GLN ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.056912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.040315 restraints weight = 111397.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.041320 restraints weight = 82218.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.041976 restraints weight = 66157.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.042590 restraints weight = 57260.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.043030 restraints weight = 51108.976| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 1.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11154 Z= 0.184 Angle : 0.654 10.802 15096 Z= 0.345 Chirality : 0.043 0.217 1596 Planarity : 0.005 0.045 1946 Dihedral : 6.667 53.068 1580 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.23), residues: 1324 helix: 0.35 (0.22), residues: 538 sheet: -1.04 (0.41), residues: 150 loop : -1.22 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 371 TYR 0.027 0.002 TYR E 45 PHE 0.018 0.002 PHE B 367 TRP 0.008 0.002 TRP A 288 HIS 0.014 0.002 HIS B 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (11152) covalent geometry : angle 0.65367 / 0.35 (15096) hydrogen bonds : bond 0.04292 / 2.76 ( 426) hydrogen bonds : angle 5.14546 / 3.53 ( 1218) metal coordination : bond 0.00258 / 0.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 240 MET cc_start: 0.6710 (ttt) cc_final: 0.6373 (ptp) REVERT: D 329 MET cc_start: 0.9036 (ttp) cc_final: 0.8562 (ppp) REVERT: A 329 MET cc_start: 0.8964 (mpp) cc_final: 0.8686 (mpp) REVERT: E 295 MET cc_start: 0.5786 (mmt) cc_final: 0.5536 (mmt) REVERT: E 350 MET cc_start: 0.5926 (ppp) cc_final: 0.5687 (ppp) REVERT: B 64 MET cc_start: 0.7036 (mtt) cc_final: 0.6547 (mtt) REVERT: B 91 MET cc_start: 0.3659 (tpt) cc_final: 0.3323 (tpp) REVERT: B 237 TYR cc_start: 0.8753 (t80) cc_final: 0.8386 (t80) REVERT: B 278 ILE cc_start: 0.9277 (mt) cc_final: 0.9011 (tt) REVERT: B 284 CYS cc_start: 0.9196 (m) cc_final: 0.8993 (m) REVERT: B 289 LYS cc_start: 0.8966 (tttm) cc_final: 0.8670 (tptt) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0879 time to fit residues: 8.7428 Evaluate side-chains 55 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 122 optimal weight: 7.9990 chunk 33 optimal weight: 30.0000 chunk 106 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 63 optimal weight: 0.3980 chunk 73 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 31 ASN ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.054644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.038609 restraints weight = 112961.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.039615 restraints weight = 83122.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.040242 restraints weight = 66889.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.040875 restraints weight = 58058.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.041219 restraints weight = 51361.208| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3604 r_free = 0.3604 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3604 r_free = 0.3604 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 1.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11154 Z= 0.224 Angle : 0.725 10.532 15096 Z= 0.387 Chirality : 0.045 0.175 1596 Planarity : 0.005 0.054 1946 Dihedral : 7.127 52.442 1580 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 21.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.22), residues: 1324 helix: -0.02 (0.22), residues: 538 sheet: -1.18 (0.41), residues: 143 loop : -1.49 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 106 TYR 0.033 0.002 TYR E 45 PHE 0.021 0.002 PHE B 367 TRP 0.011 0.002 TRP A 288 HIS 0.009 0.002 HIS B 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.22 (11152) covalent geometry : angle 0.72543 / 0.39 (15096) hydrogen bonds : bond 0.04725 / 3.08 ( 426) hydrogen bonds : angle 5.51654 / 3.78 ( 1218) metal coordination : bond 0.00333 / 0.17 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: D 329 MET cc_start: 0.9214 (ttp) cc_final: 0.8764 (ppp) REVERT: A 329 MET cc_start: 0.8995 (mpp) cc_final: 0.8750 (mpp) REVERT: E 350 MET cc_start: 0.6244 (ppp) cc_final: 0.6029 (ppp) REVERT: B 64 MET cc_start: 0.7432 (mtt) cc_final: 0.7042 (mtt) REVERT: B 91 MET cc_start: 0.4197 (tpt) cc_final: 0.3560 (tmm) REVERT: B 194 MET cc_start: 0.8737 (tmm) cc_final: 0.8383 (tmm) REVERT: B 237 TYR cc_start: 0.8852 (t80) cc_final: 0.8461 (t80) REVERT: B 278 ILE cc_start: 0.9254 (mt) cc_final: 0.9053 (tt) REVERT: B 289 LYS cc_start: 0.8953 (tttm) cc_final: 0.8601 (tptt) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0756 time to fit residues: 7.1858 Evaluate side-chains 51 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 20 optimal weight: 3.9990 chunk 105 optimal weight: 20.0000 chunk 47 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 36 optimal weight: 30.0000 chunk 12 optimal weight: 40.0000 chunk 85 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 ASN E 68 HIS ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.054908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.038823 restraints weight = 110859.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.039851 restraints weight = 80900.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.040506 restraints weight = 64772.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.041067 restraints weight = 55828.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.041543 restraints weight = 49811.640| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 1.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11154 Z= 0.180 Angle : 0.655 9.771 15096 Z= 0.347 Chirality : 0.043 0.172 1596 Planarity : 0.005 0.059 1946 Dihedral : 6.935 52.272 1580 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.23), residues: 1324 helix: 0.23 (0.22), residues: 534 sheet: -1.35 (0.40), residues: 143 loop : -1.50 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 270 TYR 0.019 0.002 TYR A 328 PHE 0.016 0.002 PHE B 75 TRP 0.011 0.002 TRP A 288 HIS 0.006 0.001 HIS B 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 (11152) covalent geometry : angle 0.65485 / 0.35 (15096) hydrogen bonds : bond 0.04386 / 2.84 ( 426) hydrogen bonds : angle 5.34679 / 3.67 ( 1218) metal coordination : bond 0.00294 / 0.15 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: D 329 MET cc_start: 0.9245 (ttp) cc_final: 0.8783 (ppp) REVERT: A 329 MET cc_start: 0.8960 (mpp) cc_final: 0.8726 (mpp) REVERT: E 51 MET cc_start: 0.8688 (pmm) cc_final: 0.8476 (pmm) REVERT: E 194 MET cc_start: 0.7589 (ptm) cc_final: 0.7352 (ptm) REVERT: E 295 MET cc_start: 0.5694 (mmt) cc_final: 0.5454 (mmt) REVERT: B 64 MET cc_start: 0.7627 (mtt) cc_final: 0.7187 (mtt) REVERT: B 91 MET cc_start: 0.4270 (tpt) cc_final: 0.3776 (tmm) REVERT: B 187 PHE cc_start: 0.6792 (m-10) cc_final: 0.6437 (m-80) REVERT: B 237 TYR cc_start: 0.8853 (t80) cc_final: 0.8491 (t80) REVERT: B 278 ILE cc_start: 0.9360 (mt) cc_final: 0.9077 (tt) REVERT: B 289 LYS cc_start: 0.9007 (tttm) cc_final: 0.8666 (tptt) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0923 time to fit residues: 8.6644 Evaluate side-chains 51 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 3 optimal weight: 0.9990 chunk 45 optimal weight: 0.0070 chunk 17 optimal weight: 7.9990 chunk 23 optimal weight: 0.0040 chunk 97 optimal weight: 9.9990 chunk 61 optimal weight: 0.2980 chunk 89 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 overall best weight: 0.4212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN B 168 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.057900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.040961 restraints weight = 105821.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.042156 restraints weight = 76429.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.043036 restraints weight = 60397.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.043609 restraints weight = 50920.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.044118 restraints weight = 45081.051| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 1.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11154 Z= 0.104 Angle : 0.560 7.087 15096 Z= 0.291 Chirality : 0.042 0.174 1596 Planarity : 0.004 0.054 1946 Dihedral : 6.310 51.506 1580 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.23), residues: 1324 helix: 0.88 (0.23), residues: 542 sheet: -1.15 (0.39), residues: 163 loop : -1.31 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 225 TYR 0.010 0.001 TYR B 23 PHE 0.016 0.001 PHE D 213 TRP 0.014 0.002 TRP D 199 HIS 0.002 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (11152) covalent geometry : angle 0.56049 / 0.29 (15096) hydrogen bonds : bond 0.03548 / 2.27 ( 426) hydrogen bonds : angle 4.76712 / 3.31 ( 1218) metal coordination : bond 0.00237 / 0.12 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2143.46 seconds wall clock time: 37 minutes 50.09 seconds (2270.09 seconds total)