Starting phenix.real_space_refine on Wed Mar 4 04:52:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ao8_11837/03_2026/7ao8_11837_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ao8_11837/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ao8_11837/03_2026/7ao8_11837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ao8_11837/03_2026/7ao8_11837.map" model { file = "/net/cci-nas-00/data/ceres_data/7ao8_11837/03_2026/7ao8_11837_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ao8_11837/03_2026/7ao8_11837_neut.cif" } 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-5986/lib/python3.9/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, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 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: 2.48, per 1000 atoms: 0.23 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: 0.80 Conformation dependent library (CDL) restraints added in 500.3 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: 0.36 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: 1.73 Time building geometry restraints manager: 1.13 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: 1.730 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.430 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3308 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 covalent geometry : bond 0.01094 (11152) covalent geometry : angle 1.51470 (15096) hydrogen bonds : bond 0.22740 ( 426) hydrogen bonds : angle 8.80789 ( 1218) metal coordination : bond 0.19074 ( 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 : 0.460 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: 0.1238 time to fit residues: 31.8586 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 : 0.428 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.081646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.062927 restraints weight = 89230.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.064265 restraints weight = 72083.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.065179 restraints weight = 60805.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.066104 restraints weight = 53561.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.066747 restraints weight = 47849.712| |-----------------------------------------------------------------------------| r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4194 r_free = 0.4194 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4195 r_free = 0.4195 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11154 Z= 0.140 Angle : 0.649 10.146 15096 Z= 0.336 Chirality : 0.045 0.401 1596 Planarity : 0.005 0.038 1946 Dihedral : 6.128 51.560 1580 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.09 % Allowed : 2.53 % 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: -0.85 (0.22), residues: 1324 helix: 0.01 (0.22), residues: 544 sheet: -0.56 (0.37), residues: 184 loop : -1.01 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 188 TYR 0.020 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 covalent geometry : bond 0.00296 (11152) covalent geometry : angle 0.64854 (15096) hydrogen bonds : bond 0.04511 ( 426) hydrogen bonds : angle 5.13571 ( 1218) metal coordination : bond 0.00142 ( 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 103 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.412 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: 0.7096 (tmm) cc_final: 0.6273 (tmm) REVERT: E 51 MET cc_start: 0.7960 (pmm) cc_final: 0.7441 (pmm) REVERT: E 242 LYS cc_start: 0.8613 (mttt) cc_final: 0.8127 (mptt) REVERT: E 245 MET cc_start: 0.8415 (mmp) cc_final: 0.7335 (tpt) REVERT: E 249 MET cc_start: 0.7385 (tpt) cc_final: 0.7036 (tpt) REVERT: E 266 LEU cc_start: 0.8521 (mt) cc_final: 0.8271 (mm) REVERT: E 324 ILE cc_start: 0.7139 (pt) cc_final: 0.6314 (pt) REVERT: B 62 GLU cc_start: 0.9233 (tp30) cc_final: 0.8986 (mp0) REVERT: B 81 PRO cc_start: 0.6539 (Cg_exo) cc_final: 0.6123 (Cg_endo) REVERT: B 141 HIS cc_start: 0.7714 (m-70) cc_final: 0.7452 (m-70) REVERT: B 152 TYR cc_start: 0.5397 (m-80) cc_final: 0.5019 (m-10) REVERT: B 259 LEU cc_start: 0.7782 (tp) cc_final: 0.7093 (tp) REVERT: B 289 LYS cc_start: 0.8420 (tttm) cc_final: 0.7924 (tptt) REVERT: B 295 MET cc_start: -0.2567 (mtt) cc_final: -0.3981 (tpp) REVERT: B 324 ILE cc_start: 0.7582 (pt) cc_final: 0.6541 (pt) outliers start: 1 outliers final: 1 residues processed: 103 average time/residue: 0.1100 time to fit residues: 16.4275 Evaluate side-chains 79 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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: 5.9990 chunk 68 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 45 optimal weight: 0.0570 chunk 100 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 overall best weight: 4.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 203 ASN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 ASN A 253 HIS ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 GLN ** 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** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN B 39 HIS B 44 ASN ** B 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 GLN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 GLN B 375 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.064359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.046549 restraints weight = 98873.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.047587 restraints weight = 77495.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.048408 restraints weight = 64630.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.049016 restraints weight = 56161.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.049404 restraints weight = 50420.742| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3814 r_free = 0.3814 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3814 r_free = 0.3814 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.7188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 11154 Z= 0.268 Angle : 0.887 11.827 15096 Z= 0.461 Chirality : 0.050 0.341 1596 Planarity : 0.006 0.061 1946 Dihedral : 7.247 58.226 1580 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % 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: -1.39 (0.22), residues: 1324 helix: -0.57 (0.21), residues: 546 sheet: -1.05 (0.38), residues: 172 loop : -1.08 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 212 TYR 0.031 0.003 TYR E 72 PHE 0.028 0.003 PHE E 198 TRP 0.022 0.003 TRP D 330 HIS 0.014 0.002 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00556 (11152) covalent geometry : angle 0.88736 (15096) hydrogen bonds : bond 0.05642 ( 426) hydrogen bonds : angle 5.73998 ( 1218) metal coordination : bond 0.00343 ( 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 87 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.424 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: D 285 MET cc_start: 0.5195 (tmm) cc_final: 0.4923 (tmm) REVERT: D 329 MET cc_start: 0.9252 (ttp) cc_final: 0.8663 (ppp) REVERT: E 51 MET cc_start: 0.8571 (pmm) cc_final: 0.8145 (pmm) REVERT: E 295 MET cc_start: 0.5195 (mmt) cc_final: 0.4870 (mmt) REVERT: B 237 TYR cc_start: 0.8104 (t80) cc_final: 0.7717 (t80) REVERT: B 241 PHE cc_start: 0.8729 (t80) cc_final: 0.7866 (t80) REVERT: B 289 LYS cc_start: 0.8638 (tttm) cc_final: 0.8299 (tptt) REVERT: B 297 MET cc_start: 0.5701 (pmm) cc_final: 0.5465 (pmm) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1070 time to fit residues: 13.8058 Evaluate side-chains 63 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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: 2.9990 chunk 6 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 15 optimal weight: 30.0000 chunk 116 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 79 optimal weight: 0.0000 chunk 98 optimal weight: 5.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 ASN E 225 ASN B 26 GLN B 39 HIS ** B 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.062945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.045340 restraints weight = 99961.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.046437 restraints weight = 76695.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.047276 restraints weight = 62872.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.047809 restraints weight = 54019.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.048119 restraints weight = 48631.543| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.7865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11154 Z= 0.156 Angle : 0.619 7.571 15096 Z= 0.326 Chirality : 0.042 0.270 1596 Planarity : 0.005 0.047 1946 Dihedral : 6.694 58.024 1580 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % 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: -0.88 (0.22), residues: 1324 helix: 0.12 (0.22), residues: 548 sheet: -0.97 (0.38), residues: 170 loop : -1.04 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 188 TYR 0.026 0.002 TYR E 303 PHE 0.012 0.002 PHE E 341 TRP 0.011 0.002 TRP A 288 HIS 0.007 0.001 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00321 (11152) covalent geometry : angle 0.61887 (15096) hydrogen bonds : bond 0.04194 ( 426) hydrogen bonds : angle 5.02094 ( 1218) metal coordination : bond 0.00281 ( 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 82 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 329 MET cc_start: 0.9074 (ttp) cc_final: 0.8811 (tpp) REVERT: A 329 MET cc_start: 0.9007 (mpp) cc_final: 0.8720 (mpp) REVERT: B 64 MET cc_start: 0.5642 (mtt) cc_final: 0.5254 (mtt) REVERT: B 237 TYR cc_start: 0.8876 (t80) cc_final: 0.8200 (t80) REVERT: B 259 LEU cc_start: 0.8164 (tp) cc_final: 0.7709 (tp) REVERT: B 263 SER cc_start: 0.8450 (t) cc_final: 0.8124 (p) REVERT: B 289 LYS cc_start: 0.8788 (tttm) cc_final: 0.8477 (tptt) REVERT: B 315 GLU cc_start: 0.9268 (mp0) cc_final: 0.8726 (tm-30) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0897 time to fit residues: 11.2566 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 : 0.281 ------------------------------------------------------------------------------- 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: 20.0000 chunk 89 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 33 optimal weight: 30.0000 chunk 104 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN D 191 GLN A 102 GLN A 132 ASN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN B 26 GLN ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 HIS ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.057394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.040884 restraints weight = 111279.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.041859 restraints weight = 82536.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.042642 restraints weight = 66740.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.043239 restraints weight = 56994.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.043605 restraints weight = 50562.182| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3665 r_free = 0.3665 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 = 0.3665 r_free = 0.3665 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 1.0090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11154 Z= 0.242 Angle : 0.776 11.102 15096 Z= 0.410 Chirality : 0.046 0.218 1596 Planarity : 0.006 0.049 1946 Dihedral : 7.302 59.135 1580 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 23.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.09 % Allowed : 3.92 % Favored : 95.99 % 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: -1.45 (0.22), residues: 1324 helix: -0.33 (0.22), residues: 525 sheet: -1.32 (0.40), residues: 154 loop : -1.34 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 371 TYR 0.037 0.003 TYR E 45 PHE 0.019 0.003 PHE B 367 TRP 0.020 0.003 TRP B 312 HIS 0.010 0.002 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00495 (11152) covalent geometry : angle 0.77568 (15096) hydrogen bonds : bond 0.05086 ( 426) hydrogen bonds : angle 5.57293 ( 1218) metal coordination : bond 0.00345 ( 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: 1 poor density : 68 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 329 MET cc_start: 0.9241 (ttp) cc_final: 0.8803 (ppp) REVERT: A 329 MET cc_start: 0.9000 (mpp) cc_final: 0.8770 (mpp) REVERT: E 295 MET cc_start: 0.5795 (mmt) cc_final: 0.5579 (mmt) REVERT: B 64 MET cc_start: 0.6546 (mtt) cc_final: 0.5936 (mtt) REVERT: B 91 MET cc_start: 0.4199 (tpt) cc_final: 0.3840 (tpp) REVERT: B 237 TYR cc_start: 0.8991 (t80) cc_final: 0.8527 (t80) REVERT: B 278 ILE cc_start: 0.9242 (mt) cc_final: 0.9025 (tt) REVERT: B 289 LYS cc_start: 0.8919 (tttm) cc_final: 0.8544 (tptt) outliers start: 1 outliers final: 0 residues processed: 69 average time/residue: 0.0936 time to fit residues: 10.0213 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 : 0.349 ------------------------------------------------------------------------------- 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: 4.9990 chunk 60 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 34 optimal weight: 30.0000 chunk 108 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN D 174 GLN E 28 HIS E 40 ASN E 375 HIS ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.058110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.041212 restraints weight = 108602.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.042324 restraints weight = 79471.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.043139 restraints weight = 63466.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.043745 restraints weight = 54077.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.044136 restraints weight = 48027.246| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 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 = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 1.0465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11154 Z= 0.162 Angle : 0.624 7.703 15096 Z= 0.332 Chirality : 0.042 0.233 1596 Planarity : 0.005 0.041 1946 Dihedral : 6.948 59.351 1580 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: -1.12 (0.22), residues: 1324 helix: 0.04 (0.22), residues: 540 sheet: -1.16 (0.41), residues: 154 loop : -1.28 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 106 TYR 0.018 0.002 TYR E 45 PHE 0.014 0.002 PHE B 75 TRP 0.013 0.002 TRP D 330 HIS 0.006 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00335 (11152) covalent geometry : angle 0.62428 (15096) hydrogen bonds : bond 0.04239 ( 426) hydrogen bonds : angle 5.16513 ( 1218) metal coordination : bond 0.00263 ( 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 63 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: D 329 MET cc_start: 0.9226 (ttp) cc_final: 0.8584 (ppp) REVERT: B 64 MET cc_start: 0.6672 (mtt) cc_final: 0.6120 (mtt) REVERT: B 237 TYR cc_start: 0.8979 (t80) cc_final: 0.8527 (t80) REVERT: B 259 LEU cc_start: 0.9016 (tp) cc_final: 0.8756 (tp) REVERT: B 278 ILE cc_start: 0.9211 (mt) cc_final: 0.9002 (tt) REVERT: B 289 LYS cc_start: 0.8959 (tttm) cc_final: 0.8652 (tptt) REVERT: B 311 CYS cc_start: 0.9682 (m) cc_final: 0.9011 (t) REVERT: B 315 GLU cc_start: 0.9344 (mp0) cc_final: 0.9005 (mp0) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0791 time to fit residues: 8.0413 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 : 0.414 ------------------------------------------------------------------------------- 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: 7.9990 chunk 124 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 89 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.057584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.040816 restraints weight = 106655.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.041874 restraints weight = 79118.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.042678 restraints weight = 63773.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.043172 restraints weight = 54282.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.043678 restraints weight = 48622.162| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 1.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11154 Z= 0.147 Angle : 0.604 7.779 15096 Z= 0.319 Chirality : 0.042 0.216 1596 Planarity : 0.004 0.043 1946 Dihedral : 6.729 57.919 1580 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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: -0.88 (0.23), residues: 1324 helix: 0.41 (0.23), residues: 538 sheet: -1.10 (0.41), residues: 154 loop : -1.28 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 55 TYR 0.026 0.002 TYR E 45 PHE 0.015 0.002 PHE B 367 TRP 0.011 0.002 TRP D 199 HIS 0.006 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00308 (11152) covalent geometry : angle 0.60365 (15096) hydrogen bonds : bond 0.04021 ( 426) hydrogen bonds : angle 5.03906 ( 1218) metal coordination : bond 0.00226 ( 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 : 0.409 Fit side-chains REVERT: D 329 MET cc_start: 0.9132 (ttp) cc_final: 0.8603 (ppp) REVERT: E 295 MET cc_start: 0.5592 (mmt) cc_final: 0.5359 (mmt) REVERT: E 350 MET cc_start: 0.5651 (ppp) cc_final: 0.5361 (ppp) REVERT: B 64 MET cc_start: 0.6762 (mtt) cc_final: 0.6229 (mtt) REVERT: B 237 TYR cc_start: 0.8890 (t80) cc_final: 0.8379 (t80) REVERT: B 289 LYS cc_start: 0.8979 (tttm) cc_final: 0.8676 (tptt) REVERT: B 311 CYS cc_start: 0.9568 (m) cc_final: 0.8848 (t) REVERT: B 315 GLU cc_start: 0.9279 (mp0) cc_final: 0.8868 (mp0) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0765 time to fit residues: 7.9021 Evaluate side-chains 57 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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: 50.0000 chunk 130 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 38 optimal weight: 30.0000 chunk 4 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 40 ASN ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 344 HIS ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** 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 = 0.4038 r_free = 0.4038 target = 0.054311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.038440 restraints weight = 113866.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.039442 restraints weight = 84398.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.040199 restraints weight = 67969.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.040642 restraints weight = 57932.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.041112 restraints weight = 52191.540| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 1.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11154 Z= 0.236 Angle : 0.744 11.123 15096 Z= 0.399 Chirality : 0.045 0.257 1596 Planarity : 0.006 0.046 1946 Dihedral : 7.375 55.127 1580 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 23.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % 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: -1.51 (0.22), residues: 1324 helix: -0.23 (0.22), residues: 544 sheet: -1.27 (0.43), residues: 143 loop : -1.58 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 55 TYR 0.026 0.003 TYR E 45 PHE 0.026 0.003 PHE E 150 TRP 0.013 0.003 TRP D 199 HIS 0.009 0.002 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00482 (11152) covalent geometry : angle 0.74361 (15096) hydrogen bonds : bond 0.04842 ( 426) hydrogen bonds : angle 5.60880 ( 1218) metal coordination : bond 0.00377 ( 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 60 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.449 Fit side-chains REVERT: D 240 MET cc_start: 0.6774 (ttt) cc_final: 0.6572 (ptp) REVERT: D 329 MET cc_start: 0.9254 (ttp) cc_final: 0.8793 (ppp) REVERT: A 329 MET cc_start: 0.8863 (mmp) cc_final: 0.8629 (mmm) REVERT: E 295 MET cc_start: 0.5993 (mmt) cc_final: 0.5695 (mmt) REVERT: E 350 MET cc_start: 0.6228 (ppp) cc_final: 0.5953 (ppp) REVERT: B 64 MET cc_start: 0.7399 (mtt) cc_final: 0.6867 (mtt) REVERT: B 91 MET cc_start: 0.3932 (tpt) cc_final: 0.3447 (tmm) REVERT: B 237 TYR cc_start: 0.8861 (t80) cc_final: 0.8465 (t80) REVERT: B 284 CYS cc_start: 0.9360 (m) cc_final: 0.9144 (m) REVERT: B 289 LYS cc_start: 0.9026 (tttm) cc_final: 0.8630 (tptt) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0861 time to fit residues: 8.4019 Evaluate side-chains 52 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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: 10.0000 chunk 33 optimal weight: 30.0000 chunk 106 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 HIS ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.054491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.038583 restraints weight = 110741.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.039547 restraints weight = 81801.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.040318 restraints weight = 66183.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.040794 restraints weight = 56300.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.041262 restraints weight = 50420.024| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 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 = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 1.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11154 Z= 0.195 Angle : 0.670 10.282 15096 Z= 0.359 Chirality : 0.044 0.235 1596 Planarity : 0.005 0.049 1946 Dihedral : 7.122 51.531 1580 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: -1.36 (0.23), residues: 1324 helix: 0.07 (0.22), residues: 526 sheet: -1.32 (0.42), residues: 143 loop : -1.60 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 36 TYR 0.023 0.002 TYR E 45 PHE 0.026 0.002 PHE D 314 TRP 0.015 0.002 TRP B 312 HIS 0.006 0.001 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00401 (11152) covalent geometry : angle 0.67050 (15096) hydrogen bonds : bond 0.04469 ( 426) hydrogen bonds : angle 5.42970 ( 1218) metal coordination : bond 0.00324 ( 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 58 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.436 Fit side-chains REVERT: C 179 TYR cc_start: 0.8167 (m-80) cc_final: 0.7917 (m-10) REVERT: D 329 MET cc_start: 0.9308 (ttp) cc_final: 0.8749 (ppp) REVERT: E 295 MET cc_start: 0.6028 (mmt) cc_final: 0.5827 (mmt) REVERT: E 350 MET cc_start: 0.6127 (ppp) cc_final: 0.5872 (ppp) REVERT: B 64 MET cc_start: 0.7526 (mtt) cc_final: 0.7033 (mtt) REVERT: B 91 MET cc_start: 0.4269 (tpt) cc_final: 0.3851 (tmm) REVERT: B 237 TYR cc_start: 0.8896 (t80) cc_final: 0.8491 (t80) REVERT: B 284 CYS cc_start: 0.9411 (m) cc_final: 0.9206 (m) REVERT: B 289 LYS cc_start: 0.9093 (tttm) cc_final: 0.8739 (tptt) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0859 time to fit residues: 8.1442 Evaluate side-chains 52 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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: 6.9990 chunk 47 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 36 optimal weight: 40.0000 chunk 12 optimal weight: 40.0000 chunk 85 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN E 68 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.054760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.038655 restraints weight = 110807.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.039718 restraints weight = 81249.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.040504 restraints weight = 65137.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.041075 restraints weight = 55241.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.041344 restraints weight = 48943.291| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 1.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11154 Z= 0.157 Angle : 0.623 9.667 15096 Z= 0.330 Chirality : 0.043 0.196 1596 Planarity : 0.005 0.053 1946 Dihedral : 6.927 54.936 1580 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % 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: -1.14 (0.23), residues: 1324 helix: 0.31 (0.23), residues: 523 sheet: -1.07 (0.44), residues: 143 loop : -1.57 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 270 TYR 0.018 0.002 TYR C 196 PHE 0.014 0.002 PHE D 213 TRP 0.010 0.002 TRP B 312 HIS 0.007 0.001 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00330 (11152) covalent geometry : angle 0.62312 (15096) hydrogen bonds : bond 0.04040 ( 426) hydrogen bonds : angle 5.24271 ( 1218) metal coordination : bond 0.00228 ( 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 : 0.424 Fit side-chains REVERT: D 329 MET cc_start: 0.9322 (ttp) cc_final: 0.8714 (ppp) REVERT: B 64 MET cc_start: 0.7513 (mtt) cc_final: 0.7105 (mtt) REVERT: B 91 MET cc_start: 0.4287 (tpt) cc_final: 0.3837 (tmm) REVERT: B 237 TYR cc_start: 0.8841 (t80) cc_final: 0.8461 (t80) REVERT: B 311 CYS cc_start: 0.9677 (m) cc_final: 0.9281 (t) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0782 time to fit residues: 7.8329 Evaluate side-chains 50 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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: 6.9990 chunk 45 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 23 optimal weight: 0.1980 chunk 97 optimal weight: 10.0000 chunk 61 optimal weight: 0.4980 chunk 89 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 86 optimal weight: 20.0000 chunk 114 optimal weight: 8.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN E 68 HIS B 95 ASN B 281 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.054021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.038310 restraints weight = 111984.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.039266 restraints weight = 82211.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.040059 restraints weight = 66776.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.040377 restraints weight = 56259.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.040944 restraints weight = 51305.765| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 1.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11154 Z= 0.171 Angle : 0.640 8.749 15096 Z= 0.340 Chirality : 0.043 0.171 1596 Planarity : 0.005 0.054 1946 Dihedral : 7.002 57.528 1580 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -1.17 (0.23), residues: 1324 helix: 0.28 (0.22), residues: 526 sheet: -1.19 (0.43), residues: 143 loop : -1.56 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 55 TYR 0.020 0.002 TYR E 45 PHE 0.016 0.002 PHE E 252 TRP 0.011 0.002 TRP D 199 HIS 0.006 0.001 HIS B 281 Details of bonding type rmsd covalent geometry : bond 0.00354 (11152) covalent geometry : angle 0.63957 (15096) hydrogen bonds : bond 0.04083 ( 426) hydrogen bonds : angle 5.33015 ( 1218) metal coordination : bond 0.00220 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2265.06 seconds wall clock time: 39 minutes 51.35 seconds (2391.35 seconds total)