Starting phenix.real_space_refine on Sun Apr 5 23:50:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y94_72688/04_2026/9y94_72688.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y94_72688/04_2026/9y94_72688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y94_72688/04_2026/9y94_72688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y94_72688/04_2026/9y94_72688.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y94_72688/04_2026/9y94_72688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y94_72688/04_2026/9y94_72688.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 9091 2.51 5 N 2267 2.21 5 O 2570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14018 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2774 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 327} Chain breaks: 1 Chain: "B" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2754 Classifications: {'peptide': 341} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 325} Chain breaks: 1 Chain: "C" Number of atoms: 2757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2757 Classifications: {'peptide': 341} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 325} Chain breaks: 1 Chain: "D" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 330} Chain breaks: 1 Chain: "E" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2766 Classifications: {'peptide': 342} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 326} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.04, per 1000 atoms: 0.22 Number of scatterers: 14018 At special positions: 0 Unit cell: (90.72, 90.72, 133.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 2570 8.00 N 2267 7.00 C 9091 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 243 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 243 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 243 " distance=2.03 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 186 " distance=2.03 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 243 " distance=2.03 Simple disulfide: pdb=" SG CYS E 172 " - pdb=" SG CYS E 186 " distance=2.03 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS E 243 " distance=2.03 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: 1.14 Conformation dependent library (CDL) restraints added in 635.1 milliseconds 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3286 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 24 sheets defined 40.4% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 43 through 52 Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 254 through 259 removed outlier: 3.792A pdb=" N ILE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 272 removed outlier: 3.705A pdb=" N SER A 265 " --> pdb=" O MET A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.681A pdb=" N TRP A 277 " --> pdb=" O TRP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 305 Processing helix chain 'A' and resid 315 through 347 Processing helix chain 'A' and resid 413 through 449 removed outlier: 3.838A pdb=" N ALA A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Proline residue: A 427 - end of helix removed outlier: 3.566A pdb=" N THR A 440 " --> pdb=" O PHE A 436 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 52 removed outlier: 3.652A pdb=" N LEU B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 127 removed outlier: 3.712A pdb=" N LEU B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASP B 125 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER B 126 " --> pdb=" O MET B 123 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 127 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 removed outlier: 3.634A pdb=" N ILE B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 277 removed outlier: 3.942A pdb=" N PHE B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TRP B 277 " --> pdb=" O TRP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.826A pdb=" N ALA B 282 " --> pdb=" O ASN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 306 removed outlier: 3.700A pdb=" N ALA B 288 " --> pdb=" O PRO B 284 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 344 removed outlier: 3.768A pdb=" N TYR B 335 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN B 344 " --> pdb=" O PHE B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 441 Proline residue: B 427 - end of helix removed outlier: 4.534A pdb=" N ILE B 439 " --> pdb=" O ILE B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 448 Processing helix chain 'C' and resid 44 through 53 Processing helix chain 'C' and resid 105 through 108 Processing helix chain 'C' and resid 120 through 127 removed outlier: 3.589A pdb=" N MET C 123 " --> pdb=" O ASP C 120 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 124 " --> pdb=" O PRO C 121 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASP C 125 " --> pdb=" O SER C 122 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE C 127 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 273 removed outlier: 3.587A pdb=" N TRP C 273 " --> pdb=" O VAL C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 278 removed outlier: 4.034A pdb=" N TRP C 277 " --> pdb=" O TRP C 273 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 278 " --> pdb=" O VAL C 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 273 through 278' Processing helix chain 'C' and resid 282 through 305 removed outlier: 3.759A pdb=" N ARG C 305 " --> pdb=" O SER C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 343 Processing helix chain 'C' and resid 412 through 449 Proline residue: C 427 - end of helix removed outlier: 3.600A pdb=" N ARG C 445 " --> pdb=" O TYR C 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 52 Processing helix chain 'D' and resid 105 through 108 removed outlier: 3.586A pdb=" N ALA D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 105 through 108' Processing helix chain 'D' and resid 120 through 127 removed outlier: 3.569A pdb=" N LEU D 124 " --> pdb=" O PRO D 121 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASP D 125 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE D 127 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 261 removed outlier: 3.580A pdb=" N ILE D 259 " --> pdb=" O GLY D 255 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN D 260 " --> pdb=" O TYR D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 278 removed outlier: 3.553A pdb=" N VAL D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TRP D 277 " --> pdb=" O TRP D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 304 Processing helix chain 'D' and resid 315 through 344 Processing helix chain 'D' and resid 409 through 449 removed outlier: 3.712A pdb=" N ALA D 424 " --> pdb=" O THR D 420 " (cutoff:3.500A) Proline residue: D 427 - end of helix removed outlier: 3.516A pdb=" N ILE D 444 " --> pdb=" O THR D 440 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG D 445 " --> pdb=" O TYR D 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 53 Processing helix chain 'E' and resid 54 through 57 removed outlier: 4.167A pdb=" N GLY E 57 " --> pdb=" O ARG E 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 54 through 57' Processing helix chain 'E' and resid 105 through 108 removed outlier: 3.775A pdb=" N ALA E 108 " --> pdb=" O SER E 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 105 through 108' Processing helix chain 'E' and resid 120 through 127 removed outlier: 3.771A pdb=" N LEU E 124 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP E 125 " --> pdb=" O SER E 122 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE E 127 " --> pdb=" O LEU E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 179 removed outlier: 4.424A pdb=" N ASN E 178 " --> pdb=" O ASP E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 261 removed outlier: 3.660A pdb=" N ILE E 259 " --> pdb=" O GLY E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 278 removed outlier: 3.698A pdb=" N SER E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE E 276 " --> pdb=" O SER E 272 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TRP E 277 " --> pdb=" O TRP E 273 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE E 278 " --> pdb=" O VAL E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 305 removed outlier: 3.651A pdb=" N ARG E 305 " --> pdb=" O SER E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 343 removed outlier: 3.923A pdb=" N LEU E 332 " --> pdb=" O VAL E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 443 removed outlier: 3.657A pdb=" N ASP E 419 " --> pdb=" O ALA E 415 " (cutoff:3.500A) Proline residue: E 427 - end of helix removed outlier: 3.693A pdb=" N PHE E 430 " --> pdb=" O PHE E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 449 Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 75 Processing sheet with id=AA2, first strand: chain 'A' and resid 116 through 119 removed outlier: 4.474A pdb=" N LEU A 152 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR A 167 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA A 140 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR A 169 " --> pdb=" O LYS A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 116 through 119 removed outlier: 4.474A pdb=" N LEU A 152 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASP A 91 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL A 85 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N PHE A 97 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 79 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ARG A 99 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ILE A 77 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 134 removed outlier: 5.337A pdb=" N THR A 242 " --> pdb=" O SER A 192 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N CYS A 243 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N GLY A 230 " --> pdb=" O CYS A 243 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU A 245 " --> pdb=" O GLU A 228 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLU A 228 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LYS A 247 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N GLU A 226 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N HIS A 249 " --> pdb=" O LYS A 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 183 through 187 removed outlier: 3.790A pdb=" N CYS A 186 " --> pdb=" O PHE A 248 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 248 " --> pdb=" O CYS A 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 116 through 118 removed outlier: 4.791A pdb=" N LYS B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASN B 103 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASN B 72 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL B 71 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLU B 203 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL B 73 " --> pdb=" O GLU B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 137 through 141 removed outlier: 6.743A pdb=" N THR B 169 " --> pdb=" O LYS B 138 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA B 140 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N THR B 167 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ASP B 91 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL B 85 " --> pdb=" O ASP B 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA9, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AB1, first strand: chain 'B' and resid 234 through 235 Processing sheet with id=AB2, first strand: chain 'C' and resid 116 through 119 removed outlier: 4.412A pdb=" N LEU C 152 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS C 159 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ASP C 91 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N SER C 84 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ARG C 93 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N PHE C 82 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASN C 95 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE C 78 " --> pdb=" O PHE C 97 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASN C 103 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN C 72 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 137 through 141 removed outlier: 6.796A pdb=" N THR C 169 " --> pdb=" O LYS C 138 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA C 140 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N THR C 167 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ASP C 91 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N SER C 84 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ARG C 93 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N PHE C 82 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASN C 95 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE C 78 " --> pdb=" O PHE C 97 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASN C 103 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN C 72 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 132 through 134 Processing sheet with id=AB5, first strand: chain 'C' and resid 132 through 134 removed outlier: 3.627A pdb=" N GLU C 245 " --> pdb=" O GLY C 230 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY C 230 " --> pdb=" O GLU C 245 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 234 through 236 Processing sheet with id=AB7, first strand: chain 'D' and resid 116 through 119 removed outlier: 3.552A pdb=" N LEU D 117 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE D 154 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU D 119 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU D 152 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS D 159 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASN D 103 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN D 72 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL D 71 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N GLU D 203 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL D 73 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 137 through 141 removed outlier: 6.899A pdb=" N THR D 169 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA D 140 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR D 167 " --> pdb=" O ALA D 140 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASP D 91 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N VAL D 85 " --> pdb=" O ASP D 91 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 132 through 134 Processing sheet with id=AC1, first strand: chain 'D' and resid 183 through 187 removed outlier: 3.738A pdb=" N GLU D 245 " --> pdb=" O GLY D 230 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY D 230 " --> pdb=" O GLU D 245 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 234 through 236 Processing sheet with id=AC3, first strand: chain 'E' and resid 116 through 118 removed outlier: 4.221A pdb=" N LYS E 159 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASN E 103 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN E 72 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL E 71 " --> pdb=" O ILE E 201 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLU E 203 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL E 73 " --> pdb=" O GLU E 203 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 137 through 141 removed outlier: 6.771A pdb=" N THR E 169 " --> pdb=" O LYS E 138 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA E 140 " --> pdb=" O THR E 167 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR E 167 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ARG E 93 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N SER E 84 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN E 95 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N PHE E 82 " --> pdb=" O ASN E 95 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN E 211 " --> pdb=" O ILE E 77 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 132 through 134 removed outlier: 3.792A pdb=" N GLU E 245 " --> pdb=" O GLY E 230 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N HIS E 249 " --> pdb=" O GLU E 226 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU E 226 " --> pdb=" O HIS E 249 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N GLU E 251 " --> pdb=" O LYS E 224 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LYS E 224 " --> pdb=" O GLU E 251 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 234 through 236 727 hydrogen bonds defined for protein. 2073 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4287 1.34 - 1.47: 3558 1.47 - 1.60: 6363 1.60 - 1.73: 0 1.73 - 1.86: 150 Bond restraints: 14358 Sorted by residual: bond pdb=" N ILE E 96 " pdb=" CA ILE E 96 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.18e-02 7.18e+03 1.07e+01 bond pdb=" N ILE A 127 " pdb=" CA ILE A 127 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.14e-02 7.69e+03 1.06e+01 bond pdb=" N ILE C 96 " pdb=" CA ILE C 96 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.18e-02 7.18e+03 1.03e+01 bond pdb=" C PRO D 69 " pdb=" O PRO D 69 " ideal model delta sigma weight residual 1.243 1.217 0.027 8.50e-03 1.38e+04 9.74e+00 bond pdb=" N ILE D 96 " pdb=" CA ILE D 96 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.23e-02 6.61e+03 9.62e+00 ... (remaining 14353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 18309 1.43 - 2.86: 985 2.86 - 4.29: 153 4.29 - 5.72: 20 5.72 - 7.15: 15 Bond angle restraints: 19482 Sorted by residual: angle pdb=" C TYR B 195 " pdb=" CA TYR B 195 " pdb=" CB TYR B 195 " ideal model delta sigma weight residual 109.37 116.19 -6.82 1.91e+00 2.74e-01 1.27e+01 angle pdb=" CA SER B 192 " pdb=" C SER B 192 " pdb=" O SER B 192 " ideal model delta sigma weight residual 121.56 117.31 4.25 1.21e+00 6.83e-01 1.23e+01 angle pdb=" CA ARG A 305 " pdb=" C ARG A 305 " pdb=" O ARG A 305 " ideal model delta sigma weight residual 122.64 118.26 4.38 1.25e+00 6.40e-01 1.23e+01 angle pdb=" CA PHE D 97 " pdb=" CB PHE D 97 " pdb=" CG PHE D 97 " ideal model delta sigma weight residual 113.80 117.17 -3.37 1.00e+00 1.00e+00 1.14e+01 angle pdb=" C ASN B 178 " pdb=" N PHE B 179 " pdb=" CA PHE B 179 " ideal model delta sigma weight residual 120.39 125.06 -4.67 1.39e+00 5.18e-01 1.13e+01 ... (remaining 19477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.27: 8173 22.27 - 44.55: 444 44.55 - 66.82: 55 66.82 - 89.09: 11 89.09 - 111.36: 3 Dihedral angle restraints: 8686 sinusoidal: 3622 harmonic: 5064 Sorted by residual: dihedral pdb=" CB CYS C 232 " pdb=" SG CYS C 232 " pdb=" SG CYS C 243 " pdb=" CB CYS C 243 " ideal model delta sinusoidal sigma weight residual 93.00 53.02 39.98 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" C3 NAG D 501 " pdb=" C1 NAG D 501 " pdb=" C2 NAG D 501 " pdb=" O5 NAG D 501 " ideal model delta sinusoidal sigma weight residual -55.55 55.81 -111.36 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" N2 NAG D 501 " pdb=" C1 NAG D 501 " pdb=" C2 NAG D 501 " pdb=" O5 NAG D 501 " ideal model delta sinusoidal sigma weight residual -178.19 -67.79 -110.40 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 8683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1517 0.041 - 0.083: 413 0.083 - 0.124: 211 0.124 - 0.165: 52 0.165 - 0.207: 22 Chirality restraints: 2215 Sorted by residual: chirality pdb=" CA VAL E 287 " pdb=" N VAL E 287 " pdb=" C VAL E 287 " pdb=" CB VAL E 287 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA VAL D 210 " pdb=" N VAL D 210 " pdb=" C VAL D 210 " pdb=" CB VAL D 210 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA VAL B 287 " pdb=" N VAL B 287 " pdb=" C VAL B 287 " pdb=" CB VAL B 287 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 2212 not shown) Planarity restraints: 2424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 305 " 0.257 9.50e-02 1.11e+02 1.15e-01 8.17e+00 pdb=" NE ARG A 305 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 305 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 305 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 305 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 286 " 0.254 9.50e-02 1.11e+02 1.14e-01 7.94e+00 pdb=" NE ARG A 286 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 286 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 286 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 286 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 99 " -0.198 9.50e-02 1.11e+02 8.87e-02 4.89e+00 pdb=" NE ARG A 99 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 99 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 99 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 99 " -0.005 2.00e-02 2.50e+03 ... (remaining 2421 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2289 2.77 - 3.30: 13425 3.30 - 3.83: 23034 3.83 - 4.37: 27286 4.37 - 4.90: 46466 Nonbonded interactions: 112500 Sorted by model distance: nonbonded pdb=" OG SER A 155 " pdb=" OD1 ASN A 157 " model vdw 2.233 3.040 nonbonded pdb=" O VAL D 269 " pdb=" OG SER D 272 " model vdw 2.233 3.040 nonbonded pdb=" O ASP B 175 " pdb=" OH TYR B 313 " model vdw 2.249 3.040 nonbonded pdb=" OD2 ASP E 120 " pdb=" OG SER E 122 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR A 89 " pdb=" OD1 ASP A 91 " model vdw 2.261 3.040 ... (remaining 112495 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 43 through 344 or resid 412 through 449 or resid 502)) selection = (chain 'B' and (resid 43 through 449 or resid 502)) selection = (chain 'C' and (resid 43 through 344 or resid 412 through 449 or resid 502)) selection = (chain 'D' and (resid 43 through 344 or resid 412 through 449 or resid 502)) selection = (chain 'E' and (resid 43 through 344 or resid 412 through 449 or resid 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.120 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14368 Z= 0.330 Angle : 0.721 7.824 19502 Z= 0.469 Chirality : 0.052 0.207 2215 Planarity : 0.006 0.115 2424 Dihedral : 13.443 111.365 5370 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.51 (0.20), residues: 1693 helix: 0.52 (0.21), residues: 582 sheet: -0.38 (0.29), residues: 365 loop : -0.91 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 99 TYR 0.014 0.001 TYR A 441 PHE 0.014 0.001 PHE E 133 TRP 0.010 0.001 TRP B 277 HIS 0.002 0.001 HIS B 143 Details of bonding type rmsd covalent geometry : bond 0.00478 (14358) covalent geometry : angle 0.71664 (19482) SS BOND : bond 0.00194 ( 10) SS BOND : angle 2.57154 ( 20) hydrogen bonds : bond 0.20978 ( 681) hydrogen bonds : angle 7.40029 ( 2073) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASN cc_start: 0.5854 (t0) cc_final: 0.5596 (t0) REVERT: A 340 PHE cc_start: 0.8299 (t80) cc_final: 0.7783 (t80) REVERT: B 196 THR cc_start: 0.7997 (p) cc_final: 0.7649 (t) REVERT: C 435 ILE cc_start: 0.9082 (mm) cc_final: 0.8814 (mm) REVERT: D 416 LYS cc_start: 0.8538 (pttp) cc_final: 0.8317 (pttp) REVERT: E 280 MET cc_start: 0.8033 (ppp) cc_final: 0.7777 (ppp) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.1072 time to fit residues: 47.9957 Evaluate side-chains 209 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 0.2980 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 GLN C 189 GLN C 344 GLN D 95 ASN D 339 ASN E 220 GLN ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.114473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.086480 restraints weight = 27870.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.089831 restraints weight = 14063.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.091996 restraints weight = 9088.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.093398 restraints weight = 6842.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.094252 restraints weight = 5678.626| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 14368 Z= 0.330 Angle : 0.712 8.398 19502 Z= 0.371 Chirality : 0.045 0.158 2215 Planarity : 0.005 0.049 2424 Dihedral : 6.658 88.588 2073 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.75 % Allowed : 10.11 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.23 (0.20), residues: 1693 helix: 1.19 (0.21), residues: 605 sheet: -0.43 (0.28), residues: 358 loop : -1.11 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 343 TYR 0.020 0.002 TYR D 256 PHE 0.044 0.002 PHE B 433 TRP 0.012 0.002 TRP B 204 HIS 0.006 0.002 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00743 (14358) covalent geometry : angle 0.71047 (19482) SS BOND : bond 0.00297 ( 10) SS BOND : angle 1.81009 ( 20) hydrogen bonds : bond 0.04822 ( 681) hydrogen bonds : angle 5.23280 ( 2073) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASN cc_start: 0.5872 (t0) cc_final: 0.5607 (t0) REVERT: B 196 THR cc_start: 0.8502 (p) cc_final: 0.8030 (t) REVERT: C 297 MET cc_start: 0.8767 (tpt) cc_final: 0.8460 (mmm) REVERT: C 435 ILE cc_start: 0.9060 (mm) cc_final: 0.8816 (mm) REVERT: C 439 ILE cc_start: 0.9445 (tp) cc_final: 0.9190 (pt) REVERT: E 280 MET cc_start: 0.8520 (ppp) cc_final: 0.7819 (ppp) outliers start: 27 outliers final: 21 residues processed: 234 average time/residue: 0.1035 time to fit residues: 37.1190 Evaluate side-chains 218 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 228 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 2 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 140 optimal weight: 0.8980 chunk 97 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.118591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.089612 restraints weight = 27184.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.093208 restraints weight = 13273.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.095564 restraints weight = 8458.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.097027 restraints weight = 6297.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.098026 restraints weight = 5224.933| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14368 Z= 0.124 Angle : 0.561 9.105 19502 Z= 0.292 Chirality : 0.041 0.151 2215 Planarity : 0.004 0.057 2424 Dihedral : 5.627 79.423 2073 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.49 % Allowed : 12.25 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.24 (0.20), residues: 1693 helix: 1.74 (0.21), residues: 588 sheet: -0.28 (0.28), residues: 362 loop : -0.87 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 305 TYR 0.018 0.001 TYR D 256 PHE 0.039 0.002 PHE E 426 TRP 0.009 0.001 TRP C 102 HIS 0.002 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00271 (14358) covalent geometry : angle 0.55843 (19482) SS BOND : bond 0.00263 ( 10) SS BOND : angle 1.69709 ( 20) hydrogen bonds : bond 0.03960 ( 681) hydrogen bonds : angle 4.72635 ( 2073) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.6727 (mtm) cc_final: 0.6278 (mtm) REVERT: A 279 ASN cc_start: 0.5995 (t0) cc_final: 0.5668 (t0) REVERT: B 196 THR cc_start: 0.8219 (p) cc_final: 0.7745 (t) REVERT: C 280 MET cc_start: 0.7206 (ppp) cc_final: 0.6579 (tpt) REVERT: C 435 ILE cc_start: 0.9071 (mm) cc_final: 0.8816 (mm) REVERT: C 439 ILE cc_start: 0.9439 (tp) cc_final: 0.9156 (pt) REVERT: D 52 MET cc_start: 0.7482 (ptp) cc_final: 0.7122 (ptm) REVERT: D 305 ARG cc_start: 0.7922 (ttp80) cc_final: 0.7721 (tmm-80) REVERT: E 90 MET cc_start: 0.8896 (mmt) cc_final: 0.8223 (mmt) REVERT: E 280 MET cc_start: 0.8487 (ppp) cc_final: 0.7961 (ppp) REVERT: E 426 PHE cc_start: 0.8152 (m-80) cc_final: 0.7833 (m-80) REVERT: E 436 PHE cc_start: 0.8551 (t80) cc_final: 0.8264 (m-80) outliers start: 23 outliers final: 12 residues processed: 227 average time/residue: 0.1062 time to fit residues: 36.7583 Evaluate side-chains 211 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 199 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain E residue 439 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 76 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 36 optimal weight: 0.0870 chunk 169 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 GLN E 220 GLN ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.118510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.089553 restraints weight = 27151.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.093091 restraints weight = 13373.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.095439 restraints weight = 8578.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.096915 restraints weight = 6411.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.097872 restraints weight = 5312.001| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14368 Z= 0.136 Angle : 0.557 9.302 19502 Z= 0.287 Chirality : 0.041 0.170 2215 Planarity : 0.004 0.046 2424 Dihedral : 5.074 60.832 2073 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.75 % Allowed : 13.87 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.44 (0.21), residues: 1693 helix: 1.86 (0.21), residues: 584 sheet: -0.19 (0.28), residues: 362 loop : -0.69 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 445 TYR 0.020 0.001 TYR D 256 PHE 0.045 0.002 PHE C 426 TRP 0.010 0.001 TRP C 102 HIS 0.003 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00305 (14358) covalent geometry : angle 0.55441 (19482) SS BOND : bond 0.00219 ( 10) SS BOND : angle 1.62211 ( 20) hydrogen bonds : bond 0.03661 ( 681) hydrogen bonds : angle 4.56790 ( 2073) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASN cc_start: 0.6065 (t0) cc_final: 0.5702 (t0) REVERT: A 297 MET cc_start: 0.8810 (tpt) cc_final: 0.8526 (mmm) REVERT: B 196 THR cc_start: 0.8260 (p) cc_final: 0.7751 (t) REVERT: C 280 MET cc_start: 0.7247 (ppp) cc_final: 0.6720 (tpt) REVERT: C 435 ILE cc_start: 0.9071 (mm) cc_final: 0.8813 (mm) REVERT: C 439 ILE cc_start: 0.9446 (tp) cc_final: 0.9158 (pt) REVERT: D 305 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7681 (tmm-80) REVERT: D 334 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8641 (tm-30) REVERT: E 90 MET cc_start: 0.8882 (mmt) cc_final: 0.8302 (mmt) REVERT: E 197 MET cc_start: 0.8972 (tpt) cc_final: 0.8569 (tpt) REVERT: E 273 TRP cc_start: 0.6815 (m-10) cc_final: 0.6522 (m-10) REVERT: E 280 MET cc_start: 0.8525 (ppp) cc_final: 0.8006 (ppp) REVERT: E 426 PHE cc_start: 0.8317 (m-80) cc_final: 0.7944 (m-80) outliers start: 27 outliers final: 19 residues processed: 231 average time/residue: 0.0979 time to fit residues: 34.3922 Evaluate side-chains 224 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 439 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 88 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.118362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.089451 restraints weight = 27306.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.092992 restraints weight = 13371.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.095336 restraints weight = 8522.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.096812 restraints weight = 6348.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.097764 restraints weight = 5258.987| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14368 Z= 0.132 Angle : 0.547 9.696 19502 Z= 0.283 Chirality : 0.041 0.168 2215 Planarity : 0.004 0.048 2424 Dihedral : 4.600 41.159 2073 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.14 % Allowed : 15.17 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.54 (0.21), residues: 1693 helix: 1.92 (0.21), residues: 585 sheet: -0.12 (0.28), residues: 362 loop : -0.63 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 445 TYR 0.022 0.001 TYR D 256 PHE 0.048 0.002 PHE C 426 TRP 0.009 0.001 TRP C 102 HIS 0.006 0.001 HIS B 446 Details of bonding type rmsd covalent geometry : bond 0.00297 (14358) covalent geometry : angle 0.54493 (19482) SS BOND : bond 0.00253 ( 10) SS BOND : angle 1.69194 ( 20) hydrogen bonds : bond 0.03462 ( 681) hydrogen bonds : angle 4.43891 ( 2073) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASN cc_start: 0.6187 (t0) cc_final: 0.5779 (t0) REVERT: A 297 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8543 (mmm) REVERT: B 191 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7840 (mm-30) REVERT: B 196 THR cc_start: 0.8141 (p) cc_final: 0.7572 (t) REVERT: C 131 ASP cc_start: 0.8559 (p0) cc_final: 0.8335 (p0) REVERT: C 280 MET cc_start: 0.7250 (ppp) cc_final: 0.6678 (tpt) REVERT: C 435 ILE cc_start: 0.9073 (mm) cc_final: 0.8810 (mm) REVERT: C 439 ILE cc_start: 0.9457 (tp) cc_final: 0.9162 (pt) REVERT: D 277 TRP cc_start: 0.8516 (m100) cc_final: 0.8288 (m100) REVERT: D 334 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8651 (tm-30) REVERT: E 90 MET cc_start: 0.8859 (mmt) cc_final: 0.8371 (mmt) REVERT: E 197 MET cc_start: 0.8953 (tpt) cc_final: 0.8544 (tpt) REVERT: E 280 MET cc_start: 0.8546 (ppp) cc_final: 0.8033 (ppp) REVERT: E 426 PHE cc_start: 0.8349 (m-80) cc_final: 0.8062 (m-80) outliers start: 33 outliers final: 20 residues processed: 231 average time/residue: 0.1006 time to fit residues: 35.9758 Evaluate side-chains 222 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 327 PHE Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 439 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 110 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 122 optimal weight: 0.3980 chunk 142 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 chunk 86 optimal weight: 0.0370 chunk 128 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.120064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.091049 restraints weight = 26975.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.094703 restraints weight = 13277.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.097034 restraints weight = 8449.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.098587 restraints weight = 6314.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.099522 restraints weight = 5187.502| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14368 Z= 0.104 Angle : 0.542 10.190 19502 Z= 0.277 Chirality : 0.041 0.156 2215 Planarity : 0.004 0.049 2424 Dihedral : 4.134 33.159 2073 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.75 % Allowed : 15.88 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.64 (0.21), residues: 1693 helix: 1.93 (0.21), residues: 585 sheet: -0.03 (0.28), residues: 361 loop : -0.52 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 305 TYR 0.030 0.001 TYR A 335 PHE 0.056 0.002 PHE C 426 TRP 0.009 0.001 TRP C 102 HIS 0.002 0.000 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00229 (14358) covalent geometry : angle 0.54003 (19482) SS BOND : bond 0.00233 ( 10) SS BOND : angle 1.39069 ( 20) hydrogen bonds : bond 0.03266 ( 681) hydrogen bonds : angle 4.28900 ( 2073) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 ASN cc_start: 0.6378 (t0) cc_final: 0.5943 (t0) REVERT: A 297 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8562 (mmm) REVERT: B 123 MET cc_start: 0.8287 (ttp) cc_final: 0.8087 (tmm) REVERT: B 191 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7628 (mm-30) REVERT: B 196 THR cc_start: 0.8011 (p) cc_final: 0.7460 (t) REVERT: B 439 ILE cc_start: 0.9065 (tp) cc_final: 0.8812 (pt) REVERT: C 280 MET cc_start: 0.7323 (ppp) cc_final: 0.6742 (tpt) REVERT: C 435 ILE cc_start: 0.9068 (mm) cc_final: 0.8792 (mm) REVERT: C 439 ILE cc_start: 0.9443 (tp) cc_final: 0.9146 (pt) REVERT: D 277 TRP cc_start: 0.8496 (m100) cc_final: 0.8272 (m100) REVERT: D 305 ARG cc_start: 0.7882 (ttp80) cc_final: 0.7612 (tmm-80) REVERT: D 334 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8700 (tm-30) REVERT: E 90 MET cc_start: 0.8815 (mmt) cc_final: 0.8349 (mmt) REVERT: E 261 MET cc_start: 0.8102 (mtt) cc_final: 0.7823 (mtm) REVERT: E 280 MET cc_start: 0.8499 (ppp) cc_final: 0.7989 (ppp) REVERT: E 426 PHE cc_start: 0.8338 (m-80) cc_final: 0.8073 (m-80) outliers start: 27 outliers final: 21 residues processed: 226 average time/residue: 0.1038 time to fit residues: 36.1485 Evaluate side-chains 225 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 327 PHE Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 439 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 GLN E 220 GLN ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.118516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.089748 restraints weight = 27215.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.093259 restraints weight = 13562.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.095553 restraints weight = 8742.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.097003 restraints weight = 6564.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.097952 restraints weight = 5448.584| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14368 Z= 0.136 Angle : 0.558 10.151 19502 Z= 0.285 Chirality : 0.041 0.152 2215 Planarity : 0.004 0.049 2424 Dihedral : 4.061 30.219 2073 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.20 % Allowed : 16.33 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.64 (0.21), residues: 1693 helix: 1.93 (0.21), residues: 585 sheet: 0.01 (0.28), residues: 362 loop : -0.53 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 305 TYR 0.025 0.001 TYR A 335 PHE 0.051 0.002 PHE C 426 TRP 0.008 0.001 TRP C 102 HIS 0.002 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00308 (14358) covalent geometry : angle 0.55611 (19482) SS BOND : bond 0.00275 ( 10) SS BOND : angle 1.43219 ( 20) hydrogen bonds : bond 0.03314 ( 681) hydrogen bonds : angle 4.32835 ( 2073) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASN cc_start: 0.6425 (t0) cc_final: 0.5977 (t0) REVERT: A 297 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8539 (mmm) REVERT: A 313 TYR cc_start: 0.8328 (OUTLIER) cc_final: 0.7459 (m-80) REVERT: B 191 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7589 (mm-30) REVERT: B 196 THR cc_start: 0.8072 (p) cc_final: 0.7513 (t) REVERT: B 308 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8653 (mt) REVERT: C 280 MET cc_start: 0.7295 (ppp) cc_final: 0.6658 (tpt) REVERT: C 435 ILE cc_start: 0.9069 (mm) cc_final: 0.8795 (mm) REVERT: C 439 ILE cc_start: 0.9453 (tp) cc_final: 0.9169 (pt) REVERT: D 277 TRP cc_start: 0.8494 (m100) cc_final: 0.8242 (m100) REVERT: D 334 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8699 (tm-30) REVERT: E 90 MET cc_start: 0.8798 (mmt) cc_final: 0.8412 (mmt) REVERT: E 261 MET cc_start: 0.8118 (mtt) cc_final: 0.7742 (mtm) REVERT: E 280 MET cc_start: 0.8499 (ppp) cc_final: 0.7997 (ppp) REVERT: E 426 PHE cc_start: 0.8320 (m-80) cc_final: 0.8076 (m-80) outliers start: 34 outliers final: 26 residues processed: 226 average time/residue: 0.1017 time to fit residues: 35.1584 Evaluate side-chains 232 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 203 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 327 PHE Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 439 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 151 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 155 optimal weight: 0.2980 chunk 127 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.119988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.090439 restraints weight = 26664.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.094151 restraints weight = 12831.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.096601 restraints weight = 8129.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.098143 restraints weight = 6032.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.099142 restraints weight = 4984.974| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14368 Z= 0.148 Angle : 0.576 10.757 19502 Z= 0.295 Chirality : 0.041 0.168 2215 Planarity : 0.004 0.050 2424 Dihedral : 4.080 28.884 2073 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.33 % Allowed : 16.53 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.63 (0.21), residues: 1693 helix: 1.90 (0.21), residues: 585 sheet: 0.02 (0.28), residues: 362 loop : -0.54 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 445 TYR 0.027 0.001 TYR D 256 PHE 0.051 0.002 PHE C 426 TRP 0.008 0.001 TRP C 102 HIS 0.003 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00339 (14358) covalent geometry : angle 0.57459 (19482) SS BOND : bond 0.00271 ( 10) SS BOND : angle 1.37707 ( 20) hydrogen bonds : bond 0.03355 ( 681) hydrogen bonds : angle 4.32606 ( 2073) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASN cc_start: 0.6403 (t0) cc_final: 0.5978 (t0) REVERT: A 297 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8578 (mmm) REVERT: A 313 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.7481 (m-80) REVERT: A 430 PHE cc_start: 0.8817 (t80) cc_final: 0.8512 (t80) REVERT: B 196 THR cc_start: 0.8131 (p) cc_final: 0.7550 (t) REVERT: B 308 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8674 (mt) REVERT: B 335 TYR cc_start: 0.8042 (t80) cc_final: 0.7522 (t80) REVERT: C 254 MET cc_start: 0.6895 (tmm) cc_final: 0.6617 (tpp) REVERT: C 280 MET cc_start: 0.7255 (ppp) cc_final: 0.6666 (tpt) REVERT: C 435 ILE cc_start: 0.9073 (mm) cc_final: 0.8796 (mm) REVERT: C 439 ILE cc_start: 0.9441 (tp) cc_final: 0.9155 (pt) REVERT: D 277 TRP cc_start: 0.8485 (m100) cc_final: 0.8190 (m100) REVERT: D 334 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8685 (tm-30) REVERT: E 90 MET cc_start: 0.8796 (mmt) cc_final: 0.8425 (mmt) REVERT: E 261 MET cc_start: 0.8153 (mtt) cc_final: 0.7718 (mtm) REVERT: E 280 MET cc_start: 0.8541 (ppp) cc_final: 0.8034 (ppp) outliers start: 36 outliers final: 24 residues processed: 228 average time/residue: 0.1059 time to fit residues: 36.6987 Evaluate side-chains 231 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 204 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 439 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 31 optimal weight: 0.1980 chunk 26 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 82 optimal weight: 8.9990 chunk 166 optimal weight: 20.0000 chunk 136 optimal weight: 0.9980 chunk 134 optimal weight: 0.2980 chunk 74 optimal weight: 0.0970 chunk 72 optimal weight: 0.2980 chunk 103 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN D 235 HIS E 220 GLN E 253 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.123863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.094317 restraints weight = 26471.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.098156 restraints weight = 12867.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.100649 restraints weight = 8150.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.102227 restraints weight = 6059.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.103194 restraints weight = 4991.336| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14368 Z= 0.104 Angle : 0.569 10.967 19502 Z= 0.289 Chirality : 0.041 0.168 2215 Planarity : 0.004 0.100 2424 Dihedral : 3.978 29.988 2073 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.43 % Allowed : 17.89 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.70 (0.21), residues: 1693 helix: 1.94 (0.21), residues: 584 sheet: 0.10 (0.28), residues: 362 loop : -0.50 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG D 305 TYR 0.025 0.001 TYR D 256 PHE 0.062 0.001 PHE C 426 TRP 0.009 0.001 TRP C 102 HIS 0.003 0.000 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00230 (14358) covalent geometry : angle 0.56595 (19482) SS BOND : bond 0.00233 ( 10) SS BOND : angle 2.01800 ( 20) hydrogen bonds : bond 0.03210 ( 681) hydrogen bonds : angle 4.22172 ( 2073) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASN cc_start: 0.6406 (t0) cc_final: 0.5961 (t0) REVERT: A 430 PHE cc_start: 0.8788 (t80) cc_final: 0.8519 (t80) REVERT: B 196 THR cc_start: 0.7916 (p) cc_final: 0.7351 (t) REVERT: B 280 MET cc_start: 0.6396 (tpt) cc_final: 0.4961 (pmm) REVERT: B 308 LEU cc_start: 0.9075 (mt) cc_final: 0.8665 (mt) REVERT: C 254 MET cc_start: 0.6924 (tmm) cc_final: 0.6583 (tpp) REVERT: C 280 MET cc_start: 0.7261 (ppp) cc_final: 0.6719 (tpt) REVERT: C 435 ILE cc_start: 0.9060 (mm) cc_final: 0.8784 (mm) REVERT: C 439 ILE cc_start: 0.9443 (tp) cc_final: 0.9164 (pt) REVERT: D 277 TRP cc_start: 0.8505 (m100) cc_final: 0.8212 (m100) REVERT: D 334 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8680 (tm-30) REVERT: E 90 MET cc_start: 0.8796 (mmt) cc_final: 0.8450 (mmt) REVERT: E 261 MET cc_start: 0.8069 (mtt) cc_final: 0.7701 (mtm) REVERT: E 280 MET cc_start: 0.8496 (ppp) cc_final: 0.7991 (ppp) outliers start: 22 outliers final: 17 residues processed: 216 average time/residue: 0.0982 time to fit residues: 32.3620 Evaluate side-chains 213 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 196 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 439 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 74 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 166 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.118421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.088756 restraints weight = 27199.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.092369 restraints weight = 13475.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.094733 restraints weight = 8686.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.096262 restraints weight = 6537.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.097213 restraints weight = 5427.400| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 14368 Z= 0.257 Angle : 0.674 10.022 19502 Z= 0.346 Chirality : 0.044 0.198 2215 Planarity : 0.004 0.051 2424 Dihedral : 4.548 27.868 2073 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.49 % Allowed : 17.89 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.50 (0.21), residues: 1693 helix: 1.85 (0.21), residues: 592 sheet: -0.16 (0.27), residues: 383 loop : -0.63 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 305 TYR 0.028 0.002 TYR A 335 PHE 0.059 0.002 PHE C 426 TRP 0.013 0.002 TRP D 438 HIS 0.006 0.001 HIS B 143 Details of bonding type rmsd covalent geometry : bond 0.00587 (14358) covalent geometry : angle 0.66904 (19482) SS BOND : bond 0.00341 ( 10) SS BOND : angle 2.51755 ( 20) hydrogen bonds : bond 0.03636 ( 681) hydrogen bonds : angle 4.56072 ( 2073) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 ASN cc_start: 0.6361 (t0) cc_final: 0.5937 (t0) REVERT: A 280 MET cc_start: 0.5339 (mtt) cc_final: 0.4847 (mtt) REVERT: A 313 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.7369 (m-80) REVERT: A 430 PHE cc_start: 0.8815 (t80) cc_final: 0.8552 (t80) REVERT: B 191 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7893 (mm-30) REVERT: B 196 THR cc_start: 0.8424 (p) cc_final: 0.7878 (t) REVERT: B 280 MET cc_start: 0.6517 (tpt) cc_final: 0.4747 (pmm) REVERT: B 308 LEU cc_start: 0.9124 (mt) cc_final: 0.8676 (mt) REVERT: C 254 MET cc_start: 0.6964 (tmm) cc_final: 0.6124 (tmm) REVERT: C 280 MET cc_start: 0.7219 (ppp) cc_final: 0.6586 (tpt) REVERT: C 435 ILE cc_start: 0.9025 (mm) cc_final: 0.8745 (mm) REVERT: C 439 ILE cc_start: 0.9385 (tp) cc_final: 0.9078 (pt) REVERT: D 277 TRP cc_start: 0.8489 (m100) cc_final: 0.8184 (m100) REVERT: D 334 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8690 (tm-30) REVERT: E 90 MET cc_start: 0.8771 (mmt) cc_final: 0.8391 (mmt) REVERT: E 280 MET cc_start: 0.8626 (ppp) cc_final: 0.7926 (ppp) outliers start: 23 outliers final: 18 residues processed: 215 average time/residue: 0.0958 time to fit residues: 31.5935 Evaluate side-chains 218 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 327 PHE Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 439 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 87 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 30.0000 chunk 113 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 HIS ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.119292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.089921 restraints weight = 26859.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.093570 restraints weight = 13191.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.095933 restraints weight = 8432.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.097492 restraints weight = 6325.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098466 restraints weight = 5219.377| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14368 Z= 0.193 Angle : 0.649 12.870 19502 Z= 0.330 Chirality : 0.043 0.190 2215 Planarity : 0.004 0.050 2424 Dihedral : 4.469 30.496 2073 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.43 % Allowed : 18.41 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.47 (0.21), residues: 1693 helix: 1.86 (0.21), residues: 592 sheet: -0.21 (0.27), residues: 383 loop : -0.65 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 305 TYR 0.027 0.002 TYR A 335 PHE 0.058 0.002 PHE C 426 TRP 0.012 0.001 TRP D 438 HIS 0.003 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00442 (14358) covalent geometry : angle 0.64513 (19482) SS BOND : bond 0.00302 ( 10) SS BOND : angle 2.25369 ( 20) hydrogen bonds : bond 0.03543 ( 681) hydrogen bonds : angle 4.53191 ( 2073) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2096.07 seconds wall clock time: 37 minutes 6.64 seconds (2226.64 seconds total)